Build a Second Brain with M365 Copilot

Centralize project docs and meetings into an AI-powered knowledge base.

Introduction

30 Second Summary

Every project manager knows the pain of scattered knowledge. Meeting notes live in one app, budgets in another, and status decks in a third.

In this project, you will build an AI-powered "second brain" for one of your real projects using Copilot Notebooks. It will centralize your documents, meeting notes, and data so anyone on your team can ask it questions and get structured, project-aware answers.

What You'll Build

Picture asking "What are the open risks across all our documents?" and getting back a formatted risk table with owners, priorities, and mitigation status, pulled from every file your team has added to your shared project brain.

By the end of this project, you'll have:

A working knowledge base where you ask natural language questions and get context-aware answers grounded only in your real project documents, meeting notes, and data.
A shared notebook where teammates can add their own documents and everyone queries the same custom-trained project brain with structured, formatted responses.
Copilot-generated charts and PivotTables in Excel, built from your project data using natural language prompts and Agent Mode.
An optional Secret Mission to push your skills further.

Are there any prerequisites?

This project requires a Microsoft 365 Copilot enterprise license, Windows 11 with OneNote installed, and existing project documents (Word, PowerPoint, Excel) or Teams meeting history. You will use your own real project materials throughout.

Before We Start

Before you dive in, take a moment to commit to what you're about to build and why it matters for your workflow.

Verify Your Copilot Toolkit

Copilot Notebooks is a newer feature in the Microsoft 365 ecosystem. It requires a specific version of OneNote and the right license entitlements, so not every machine has it ready out of the box.

Before you build anything, you need to confirm that Copilot Notebooks is accessible in both OneNote and the Microsoft 365 Copilot web app. You will run three quick checks in this step to make sure your toolkit is ready.

In this step, get ready to:

Confirm Copilot Notebooks appears in OneNote.
Access the Notebooks dashboard in the Microsoft 365 Copilot app.
Verify that Copilot is active inside a OneNote notebook.

Find Copilot Notebooks in OneNote

Copilot Notebooks lives inside OneNote as a dedicated section. If it appears in your notebook list, your OneNote version and license are both good to go.

Press the Windows key to open your search bar.
Type OneNote and press Enter to open it.
Look at the top of your notebook list for a Copilot Notebooks section.

✔️ I see Copilot Notebooks in my notebook list

Your OneNote version and license are ready. Move on to the next check.

ⓧ I don't see a Copilot Notebooks section

There are two common reasons this section might not appear.

If you are using the horizontal tabs layout in OneNote, Copilot Notebooks will not appear as a section on the left. Check the notebook dropdown list instead.
Copilot Notebooks requires OneNote on Windows Version 2504 (Build 18827.20128) or later. Check for updates by selecting File, then Account, then Update Options, then Update Now.
You also need a Microsoft 365 Copilot license plus a SharePoint or OneDrive license (service plan). Contact your IT administrator if you are unsure about your license entitlements.

After updating or confirming your license, restart OneNote and check for the Copilot Notebooks section again.

What is Copilot Notebooks?

Copilot Notebooks is an AI-powered workspace where you add specific documents, meeting notes, and data as references. Copilot then answers questions grounded only in those references, not your entire OneDrive or email.

Think of it as a focused brain that knows only what you feed it. The more relevant documents you add, the better its answers become.

Access the Notebooks dashboard in your browser

Copilot Notebooks also has a web interface inside the Microsoft 365 Copilot app. You will use both the OneNote and web experiences throughout this project, so you need to confirm the web dashboard loads too.

Open your browser.
Go to m365.cloud.microsoft.
Sign in with your work account.
In the left navigation pane, select Notebooks.

✔️ I see the Notebooks dashboard

The Notebooks dashboard loaded successfully. You are signed in and ready to go.

ⓧ I don't see Notebooks in the left navigation

The Notebooks option can sometimes be hidden from the default left navigation. Here is the fallback path.

At the top of the left navigation pane, select the app launcher (the grid icon, sometimes called the waffle menu).
Select Notebooks from the list.

If you still do not see Notebooks anywhere, confirm with your IT administrator that your account has a Microsoft 365 Copilot license assigned.

Confirm Copilot is active in OneNote

The final check confirms that Copilot itself is active inside OneNote. You will open the Copilot pane from the ribbon to verify your license is valid and ready to use.

Switch back to OneNote.
Open any existing notebook from your notebook list.
Look for the Copilot icon in the ribbon at the top of the window.

Before you click it, take a guess. Based on the checks you have passed so far, do you think the Copilot pane will open successfully?

Select the Copilot icon to open the Copilot pane.

✔️ The Copilot pane opens

The Copilot pane appears on the right side of your notebook. Your license is active and Copilot is ready to use. All three checks are complete.

ⓧ I don't see a Copilot icon in the ribbon

A missing Copilot icon usually means your license has not been applied to OneNote yet.

Close and reopen OneNote. License changes sometimes require a restart to take effect.
Confirm you are signed into OneNote with the same work account you used to access m365.cloud.microsoft. Select File, then Account to check which account is active.
If the icon still does not appear after restarting, contact your IT administrator to confirm that the Microsoft 365 Copilot license is assigned to your account.

You should now see the Copilot pane open on the right side of your OneNote notebook. This confirms that Copilot Notebooks is available in OneNote, the Notebooks dashboard is accessible in your browser, and your Copilot license is active.

Why check both OneNote and the web app?

Both the OneNote desktop app and the web app at m365.cloud.microsoft can open the same Copilot Notebook. The OneNote experience gives you a fuller workspace, while the web app is useful for quick access from any browser.

Your toolkit is confirmed and ready. Next up, you will create your first Copilot Notebook and load it with your real project documents.

Create Your Project Brain

Your Copilot toolkit is confirmed and ready. Now it's time to build the brain itself.

Your project knowledge is scattered across Word documents, PowerPoint decks, Excel files, and Teams meetings right now. In this step, you'll create a Copilot Notebook that pulls all of these together so Copilot can reason across your full project picture.

In this step, get ready to:

Create a new Copilot Notebook with a clear project name.
Add your real project documents and Teams meeting content as references.
Ask your first question to verify Copilot can reason across all your references.

Create your Copilot Notebook and add project files

Each Copilot Notebook scopes Copilot's knowledge to only the references you explicitly add. Your second brain will know exactly what you feed it and nothing else.

In the Copilot Notebooks section in OneNote, select New notebook.
Give your notebook a clear project name. For example, Q3 Product Launch Brain or Infrastructure Migration Hub.
Under Add content to References, browse the files that Copilot suggests from your recent work data.
Add 3-5 of your actual project documents. Include at least one Word document, one PowerPoint deck, and one Excel file.
If you don't see a file you need, select Search to find it by name, select Upload to add a local file, or drag and drop files directly into the references area.
Select Create.

Your new notebook opens with all your added references listed.

What is a Copilot Notebook?

A Copilot Notebook is an AI-powered workspace where you curate specific files as references. Copilot reasons exclusively across those references when answering your questions.

This is different from regular Copilot Chat, which searches broadly across your Microsoft 365 data. Your notebook only uses what you explicitly add, giving you precise control over your second brain's knowledge.

Why Copilot Notebooks instead of regular Copilot Chat?

Regular Copilot Chat can pull in irrelevant results or miss context buried in specific project documents. Copilot Notebooks let you curate exactly which files Copilot reasons over, so every answer is grounded in your chosen materials.

Not seeing the files you expected?

Copilot suggests files based on your recent work activity. If a specific file does not appear, select Search and type the file name directly.

Supported file types include .docx, .pptx, .xlsx, .pdf, .txt, and .rtf. If your file is in a different format, convert it before uploading.

Can't find your project files in Copilot's suggestions?

Add your Teams meeting content

Teams meetings capture decisions, action items, and context that often never make it into formal documents. Adding meeting transcripts gives your second brain access to this otherwise lost information.

In your notebook, select Add references.
Select the Meetings filter to find recent Teams meetings related to your project.
Add 1-2 meeting transcripts or notes from your project.

The meeting references now appear alongside your document references in the notebook.

How does my license affect available references?

Your enterprise Microsoft 365 Copilot license gives you access to premium sources including Teams, SharePoint, and OneDrive content. Teammates with only a Copilot Chat license can access standard sources like PDF, Word, Excel, and PowerPoint files, but not premium sources like Teams content.

Working with Power BI reports?

Power BI .pbix files are not a supported reference type. Export your Power BI reports as PDF first, then upload the PDF as a reference.

Verify your second brain with a test query

Your notebook now contains documents and meeting content from your project. Time to see if Copilot can connect the dots across all of them.

Before you ask your first question, think about it: do you expect Copilot to mention content from every single reference you added, or just a few?

In the Copilot chat area of your notebook, type What topics are covered across my references? and press Enter.

Copilot analyzes your references and returns a summary of the topics covered. The response should mention content from at least two different documents you added.

What should I see?

Copilot's response pulls themes and topics from across your references. You should see it mention specific content from your Word documents, PowerPoint decks, Excel data, or meeting notes.

If it only references one file, try a more specific prompt like "Summarize the key themes from each of my reference files." This encourages Copilot to pull from every reference individually.

Copilot's response doesn't mention your documents?

Make sure you selected Create after adding your references during notebook creation. If you closed the creation flow early, your references may not be saved.

Check that your references finished uploading. Large files may take a moment to process before Copilot can reason over them.

My Copilot Notebook isn't referencing the documents I added. How can I fix this?

Your second brain is alive and pulling from your real project data. Next up, you'll teach it how you think about your project so it stops giving generic answers and starts responding like a project management analyst.

Train Your Second Brain

Your second brain is loaded with real project documents, meeting notes, and data. In the last step, you verified it can reason across all of them at once.

Pulling the right information is only half the story. The format matters just as much. Ask your second brain for project risks right now and you'll get a wall of text instead of a structured risk register. In this step, you'll discover that gap firsthand and then close it.

In this step, get ready to:

Experience how your second brain responds to project management questions by default.
Configure custom instructions that teach Copilot your preferred response format.
Verify that the same questions now produce structured, actionable responses.

Ask your second brain for project insights

Your Copilot Notebooks brain has all the raw knowledge it needs. Before you change anything, let's see how it handles real project management questions out of the box.

In your Copilot Notebook in OneNote, type this prompt in the chat area:

What are the key risks mentioned across all my project documents and meeting notes?

Review the response. Copilot pulls relevant information from your references, but notice the format. It comes back as generic paragraphs. There's no distinction between resolved and unresolved risks, no priority levels, and no use of your project terminology.

Now try a second question. Type this prompt:

List all open action items and owners from my meeting notes and documents.

Same problem. The content is accurate, but it arrives in a conversational paragraph with no structure. No owner column, no due dates, no priority levels.

What just happened?

Your second brain knows the facts, but it does not know how you think about your project. Without guidance, Copilot formats every response like a general-purpose assistant.

That gap between "accurate content" and "useful format" is exactly what you'll fix next.

Set up custom instructions

Custom instructions are a set of rules you give your Copilot Notebook so it knows exactly how to format every response. Think of them as a style guide for your second brain.

Select the arrow next to your notebook name in the upper-left corner of your Copilot Notebook.
Select Copilot instructions.

A dialog opens where you can type instructions that shape every response your second brain gives. Copy the following template into the instructions field, then customize it to match your actual project terminology and preferred formats:

You are a project management analyst for this project.

When listing risks, format them as a table with columns for Risk, Likelihood, Impact, Owner, and Mitigation Status.

When listing action items, include Owner, Due Date, Priority (High/Medium/Low), and Status.

When creating status summaries, use our standard format: Executive Summary, Key Accomplishments, Risks and Issues, Next Steps.

Always flag items that are overdue or at risk.

Use concise, professional language.

What do these instructions do?

The first line sets a persona. Copilot now approaches every question as a project management analyst, not a general assistant.
The table definitions (risks, action items) tell Copilot exactly which columns to use. This eliminates the wall-of-text problem you saw a moment ago.
The status summary format gives Copilot a template it applies every time you ask for a project update.
The flagging rule ensures overdue or at-risk items are called out automatically, so nothing slips through.

Customize the instructions to match your project's terminology and your preferred formats.
Select Save.

You can edit instructions at any time

Custom instructions are not permanent. If a response format is not quite right, go back to Copilot instructions and refine them. You can tweak column names, add new rules, or change the persona at any time.

Compare the before and after

Your custom instructions are saved. Now it's time to see if they actually changed anything.

Before you re-ask your question, take a moment to predict: do you think the response will look different this time? What format do you expect?

Type the exact same risk question you asked earlier:

What are the key risks mentioned across all my project documents and meeting notes?

This time, Copilot responds with a structured table. You should see columns for Risk, Likelihood, Impact, Owner, and Mitigation Status. Compare this to the wall of text you got earlier. The content comes from the same references, but the format is now immediately actionable.

Now test a status summary. Type this prompt:

Create a project status summary I can share with my stakeholders.

The output should follow the structure you defined: Executive Summary, Key Accomplishments, Risks and Issues, Next Steps. You can copy this response and paste it directly into a Word document or email.

Why does this matter?

Without custom instructions, you would need to re-explain your preferred format every single time you ask a question. Custom instructions apply automatically to every response in this notebook, so your second brain always speaks your language.

Response still looks like generic paragraphs?

Confirm you selected Save after entering your custom instructions. Unsaved instructions are not applied.
Re-open the instructions dialog to verify your text is still there. Select the arrow next to your notebook name, then Copilot instructions.
Try asking your question again in a new message. Copilot applies instructions to new responses, not retroactively to older ones.

Still not working? Help me figure out why my Copilot Notebook custom instructions are not being applied to responses.

Your second brain now thinks like a project analyst. Every question you ask gets a structured, actionable response grounded in your actual project data. Next up, you'll share this brain with your team so they can feed in their own documents and get the same high-quality answers.

Share Your Brain with Your Team

Your second brain now gives structured, project-analyst responses thanks to the custom instructions you configured. But it is only as complete as what you alone know and remember to add.

Sharing your Copilot Notebook with teammates means they can contribute their own documents, meeting notes, and data. Everyone on the team gets the same structured, project-aware answers.

In this step, get ready to:

Share your Copilot Notebook with a teammate.
Confirm your teammate can access the notebook and its references.
Review the sharing considerations for your team.

Invite a teammate to your notebook

To turn your solo second brain into a team resource, you need to invite at least one teammate to your notebook.

In your project Copilot Notebook in OneNote, select the Share button in the upper right corner.
Enter the name or email address of the teammate you want to invite.
Select Invite.

An Invite successful confirmation message appears with a list of invitees. The people icon next to the Share button updates to show that at least one person now has access.

What happens to your referenced files?

When you share a notebook, recipients are automatically invited to all linked files so Copilot can provide grounded answers right away.

You must have sharing permissions for each linked file. If you do not, some linked files may remain restricted, and your teammate will need to request access to those files individually.

Not seeing the Invite confirmation?

Make sure you are signed in with the account that created the notebook.
Check that you entered a valid name or email address from your organization's directory.

Still stuck? Help me troubleshoot sharing my Copilot Notebook with a teammate.

Confirm your teammate has access

Sharing is not complete until your teammate opens the notebook and can see your references. What do you think they will see when they first open it?

Ask your teammate to open OneNote and look under the Copilot Notebooks section.
Have them filter by Shared with you to find your notebook.
Alternatively, they can go to m365.cloud.microsoft and select Notebooks in the left navigation, then filter by Shared.
Once they open the notebook, ask them to confirm they can see the references you added.

Your teammate should see all the references you added and the Copilot chat area. They can also add their own references by selecting Add references and uploading or searching for their documents.

Teammate can't find the notebook?

In OneNote, make sure they check under the Copilot Notebooks section and filter by Shared with you.
In the Microsoft 365 Copilot app, they should look under Notebooks and filter by Shared.
Make sure your teammate has a Microsoft 365 Copilot or Copilot Chat license. Without one, they cannot access Copilot Notebooks.

Still having trouble? Help my teammate find a shared Copilot Notebook.

Every new reference your teammate adds enriches the brain for the whole team.

Can teammates change the custom instructions?

Yes. Anyone with access to the notebook can view and edit the custom instructions you configured. This means the team can collaboratively refine how Copilot responds over time.

Note the sharing considerations for your team

There are a few limitations to keep in mind as your team starts collaborating on the shared notebook.

All invited teammates get editing access. There is no read-only option currently.
Group-based sharing (such as adding a Microsoft 365 group or Teams channel) is not supported. You need to invite individuals by name or email.
Teammates with only a Copilot Chat license can access standard sources like PDF, Word, Excel, and PowerPoint. They cannot access premium sources like Teams content or SharePoint.
If your notebook includes any OneNote sections or pages as references, share the underlying OneNote notebook separately so teammates can access that content.

Why do license types matter here?

If your team spans multiple license types, some teammates may not be able to see premium references like Teams meeting transcripts. You can work around this by exporting premium content as PDF before adding it, so all teammates can access it regardless of their license.

Your second brain is now a team resource that anyone can query and feed with new documents. Next up, you will use Copilot in Excel to analyze your project data and generate visualizations directly in your workbook.

Analyze Project Data with Copilot in Excel

Your second brain is now a shared project hub. Teammates can add their own documents, and everyone queries the same knowledge base for structured, project-aware answers.

Project management also requires analyzing numbers. Budgets, timelines, resource allocation, and KPIs all live in spreadsheets.

Copilot Agent Mode in Excel lets you analyze this data with natural language. It creates charts, formulas, and PivotTables directly in your workbook without you writing them manually.

In this step, get ready to:

Open a project Excel workbook and enable Copilot's editing mode.
Use Agent Mode to generate charts and PivotTables from your data with natural language.
Ask follow-up questions and learn when to use edit, plan, and chat modes.

Open your project workbook and enable Copilot

Before Copilot can analyze your data, you need to open a workbook and switch Copilot into a mode where it can make changes directly.

Open one of your project Excel workbooks that contains data you want to analyze. This could be a budget tracker, project timeline, resource allocation sheet, or KPI dashboard.
Select the Copilot icon in the Excel ribbon to open the Copilot pane.
Look for the mode switcher above the prompt box.
Confirm it shows Allow editing as the active mode.
If it shows Chat only, select it and switch to Allow editing so Copilot can work directly in your workbook.

You should see the Copilot pane open on the right side of your Excel window with Allow editing shown above the prompt box.

What do the Copilot modes mean?

The mode switcher controls how Copilot interacts with your workbook. There are three modes.

Edit mode (labeled Allow editing) lets Copilot make changes directly in your workbook, like adding formulas, charts, and PivotTables.
Chat mode (labeled Chat only) keeps all responses in the chat pane without touching your data.
Plan mode lets Copilot outline its approach before making any edits, so you can review and approve first.

Don't see the Copilot icon in the ribbon?

Make sure you are signed into Excel with your work account that has a Microsoft 365 Copilot license.
Check that your Excel version is up to date. Copilot features require current builds of Microsoft 365 apps.

Why isn't the Copilot icon showing in my Excel ribbon?

Analyze your data with Agent Mode

Agent Mode goes beyond simple chat. Instead of just answering questions about your data, Copilot takes multi-step actions directly in your workbook.

Select Agent Mode from the Tools menu in the Copilot pane.
Type an outcome-based prompt that matches your data. For example: "Analyze this data and find important insights for project decision-making. Create charts to visualize the key trends."

Before you press Enter, take a moment to predict: what kind of analysis do you think Copilot will create from your data?

Press Enter to submit your prompt.

Copilot reasons through your request step by step. You can see its reasoning logic in the pane as it examines your data structure, creates PivotTables, and builds charts.

Review your workbook. You should see at least one new chart or PivotTable that Copilot created directly on your worksheet.
Check the sheet tabs at the bottom. Copilot marks modified sheets with a green tab indicator and highlights modified cells on the grid.

Why Agent Mode instead of regular chat?

Regular chat mode can answer questions about your data, but it cannot change anything in your workbook. Agent Mode can take multi-step actions: creating PivotTables, building charts, applying formulas, and adding new sheets.

The results appear as standard Excel objects you can edit, move, and format. Copilot does the analysis, and you keep full control.

Don't see Agent Mode in the Tools menu?

Agent Mode is not yet available in the EU or UK. If you are in one of these regions, you can still use Copilot in Allow editing mode to request charts and analysis, but the multi-step Agent Mode workflow will not appear.
Make sure Allow editing is selected in the mode switcher. Agent Mode requires edit permissions to be enabled.

Why can't I find Agent Mode in Copilot for Excel?

Dig deeper with follow-up questions

Agent Mode remembers the context of your conversation. Each follow-up question builds on the previous analysis, so you can drill into specific areas without re-explaining your data.

In the Copilot pane, type a follow-up question that digs deeper into something specific. For example: "What areas are over budget?" or "Show me the resource allocation breakdown by team."
Press Enter to submit.

Copilot adds more insights, charts, or tables to your workbook based on your question. Each response builds on the previous analysis.

Undo Copilot's changes

Press Ctrl+Z to undo any changes Copilot made to your workbook. You can also check version history to restore a previous state.

When to use plan mode

If you want Copilot to explain its approach before making any edits, switch to plan mode using the mode switcher above the prompt box.

Plan mode lets you review and approve each step Copilot will take before it changes anything. This is useful when working with critical data you do not want accidentally modified.

Take a moment to think: across your initial prompt and follow-up question, how many new elements did Copilot add to your workbook?

Review your workbook tabs and sheets. You should see at least one chart or PivotTable from your initial prompt, plus additional analysis from your follow-up question. Modified sheets have a green tab indicator at the bottom.

Copilot's analysis doesn't match your data?

Make sure your data has clear column headers. Copilot uses headers to understand the structure of your data.
Try a more specific prompt. Instead of "analyze this data," name the columns or metrics you care about.
Press Ctrl+Z to undo and try a different prompt.

Why is Copilot Agent Mode giving inaccurate results for my Excel data?

Secret mission

Build a Cross-Project Knowledge Hub

Your second brain is powerful for a single project. But what if you could zoom out across your entire portfolio? In this secret mission, you will generate an audio briefing of your project notebook and build a higher-level knowledge hub that spans multiple projects.

Clean Up Your Resources

This project runs entirely on your existing Microsoft 365 Copilot enterprise license, so there are no ongoing costs from anything you created. Decide whether to keep your notebooks active, pause by revoking shared access, or delete them entirely.

Resources you used:

Your project Copilot Notebook (e.g., "Q3 Product Launch Brain") with references, custom instructions, and shared access.
Your portfolio Copilot Notebook (e.g., "Portfolio Overview") with cross-project references and custom instructions.
Copilot-generated charts and PivotTables in your project Excel workbook.

Keep everything running

No action needed. Choose this if you plan to keep using your Copilot Notebooks as a living project hub for your team.

Your project Copilot Notebook stays shared with your teammates. They can continue adding references and querying the brain.
Your portfolio Copilot Notebook stays available for cross-project queries.
Your Excel workbook retains all Copilot-generated charts and PivotTables.
Consider adding new references to your notebooks weekly to keep them current as your projects evolve.

Pause - I'll come back to this later

Revoke shared access to your notebooks so teammates cannot make changes while you are away. Your notebooks and their content stay intact for when you return.

Open your project Copilot Notebook in OneNote.
Select the Share icon in the upper-right corner.
Under Shared with, right-click each teammate's name and select Stop sharing.
When you are ready to resume, re-invite your teammates using the same Share button.
Your portfolio Copilot Notebook and Excel workbook do not need any changes. They remain in your account ready to use.

Delete - I don't want to use this again

Remove all project resources you created during this project. This frees up space and removes shared access for teammates.

Deletion is permanent

Deleting a Copilot Notebook is permanent and cannot be undone. Make sure you have copied any responses or insights you want to keep before deleting.

Open OneNote and go to the Copilot Notebooks section.
Hover over your project Copilot Notebook name and select More actions.
Select Delete, then select Delete again in the confirmation dialog.
Repeat for your portfolio Copilot Notebook. Hover over the notebook name, select More actions, then select Delete and confirm.
Open your project Excel workbook. Press Ctrl+Z repeatedly to undo the charts and PivotTables Copilot created, or check version history to revert to a version before your Copilot edits.
Your original project documents (Word, PowerPoint, Excel files) and Teams meeting content are not affected by deleting the notebooks. Those files remain in their original locations.

Nice Work!

Nice work! You just built a team-wide, AI-powered second brain for project management using Microsoft 365 Copilot.

You've learned how to:

Built and shared a Copilot Notebook that gives your whole team AI-powered, context-aware answers grounded in your real project documents, Teams meetings, and data.
Configured custom instructions that transform generic AI responses into structured project management analysis with tables, priorities, and status categories.
Used Copilot Agent Mode in Excel to analyze project data and generate charts and PivotTables with natural language prompts.
Secret Mission: Created a cross-project portfolio notebook and generated an audio overview for on-the-go project briefings.

Ready to quiz yourself?