How to Move Your Notion Workspace to a Private, Encrypted App Without Losing a Single Page

You built your whole life inside Notion. Meeting notes, project trackers, the half-finished novel, tax PDFs, screenshots you dropped in and forgot about. Then one day it hits you: none of that actually lives on your machine. It lives on Notion's servers, in plain text, and you are renting access to your own brain. This guide walks you through moving all of it onto your own disk, encrypted, in a way where nothing gets left behind and nothing stays on someone else's cloud.

I will use Filarr as the destination because it is built exactly for this (notes plus files plus a graph that links them, with per-file encryption), but most of the method here transfers to any local-first tool. The goal is simple: end the migration owning a complete, searchable, encrypted copy of everything, with zero orphaned attachments and zero broken pages.

Quick Answer: To migrate from Notion without losing data, export your entire workspace from Notion (Settings, then Export all workspace content, choosing Markdown and CSV, and enabling subpages and files). You get a ZIP containing one Markdown file per page plus every attachment. Drop that folder into Filarr's file manager and every file becomes encrypted on your disk with AES-256-GCM, one key per file. To turn pages into editable notes rather than static files, use Filarr's notes Import Wizard. Keep the original ZIP as a backup until you have verified page counts and attachments match.

Why bother leaving Notion at all

Be honest about the reason, because it changes how carefully you migrate. If you are leaving because you want speed and offline access, a rough export is fine. If you are leaving because you care about privacy and ownership, the migration itself is the whole point, and it deserves care.

The uncomfortable detail most people never check: Notion stores your pages in plain text on its infrastructure. That is normal for a SaaS product, and it is also exactly why an encrypted, local-first app exists. Filarr flips the default. Files live on your disk, each one encrypted with AES-256-GCM under its own key, and the cloud only follows if you choose to turn on sync. So the migration is not just a copy job. It is the moment your knowledge base stops being readable by anyone but you.

That framing matters for one practical reason: you want a migration that is complete, because you are about to encrypt everything and (eventually) delete the Notion original. Half a migration is worse than none.

Step 1: Export everything from Notion, the right way

Notion's export is decent but it has traps. Do this from a desktop browser, not the mobile app.

Go to Settings, then look for the workspace export option (often under Settings and members, then in the general settings area, labelled Export all workspace content). You will be offered a format choice. Pick Markdown & CSV. Markdown is the format that survives: it is plain text, every other tool reads it, and it will not rot in five years the way a proprietary format can. HTML is the alternative and it preserves slightly richer formatting, but it is heavier and messier to reuse. If you are unsure, export twice, once as Markdown and once as HTML, and keep both. Storage is cheap, regret is not.

Three settings make or break the migration:

Include subpages. Turn this on. Without it you export only the top level and silently lose everything nested underneath, which in Notion is usually most of your content.
Include files and media. Turn this on so your images, PDFs and attachments come down with the pages instead of staying as dead links.
Export scope. If you have multiple workspaces or teamspaces, export each one. Notion will not bundle them for you.

Notion emails you (or hands you directly) a ZIP file. For a large workspace this can take a while and can arrive split into several ZIPs. Download all of them. Do not start deleting anything in Notion yet. We verify first, delete last.

Step 2: Understand what you actually got

Unzip one of the archives and look inside before you import anything. This five-minute look saves hours later. You will typically see:

One .md file per page, with the page title in the filename.
A folder next to each page that had subpages or attachments, holding those children and media.
.csv files for every Notion database, one row per database entry, plus a folder of the individual entry pages.
Notion's trademark quirk: a long hexadecimal ID glued onto every filename, so "Project Roadmap" becomes something like "Project Roadmap a1b2c3d4e5f6.md".

That trailing ID is the single most annoying thing about a raw Notion export. If you just dump the files somewhere, every note is named with gibberish on the end. Good importers strip it automatically. Filarr's Notion importer, for instance, cleans those hex suffixes so "Project Roadmap a1b2c3d4e5f6" comes back as simply "Project Roadmap". Keep this in mind when you choose your import path below, because it is the difference between a tidy workspace and a thousand ugly filenames.

Also note what does not survive cleanly, so you are not surprised. Notion databases export as a CSV plus a page per row. You keep all the data, but the live machinery (formulas, rollups, relations, filtered views) does not travel. No tool can fully recreate Notion's database engine from a flat export, and anyone who promises otherwise is selling you something. Plan to keep the CSVs, which open anywhere, and rebuild only the few views you genuinely use day to day.

Step 3: Get everything onto your disk, encrypted (the safe path that never loses data)

This is the step that guarantees the "without losing data" promise, so do it first, before any fancy conversion.

Open Filarr and create (or open) a workspace. Then bring your unzipped Notion export into the file manager. You can drag the whole folder in, or use the upload action inside a folder. Filarr supports 51+ file formats, so your Markdown, PDFs, images, CSVs, and the odd .docx or .xlsx all come in as first-class files rather than being rejected or flattened.

Here is what happens under the hood, and why it is the safe path: the moment a file lands in your vault, Filarr encrypts it with AES-256-GCM using a unique key per file. The key for each file is itself wrapped by a key derived from your password (PBKDF2-SHA512 at 600,000 iterations, the OWASP 2024 recommendation, with Argon2id available as an option). Nothing is stored in the clear. So even before you have converted a single page into a pretty note, you already have a complete, encrypted, offline copy of your entire Notion life. If you stop right here, you have already won the privacy fight.

A practical tip: recreate your Notion structure as folders as you go, or just drop the export in wholesale and reorganize later. Filarr lets you move files and folders around with drag-and-drop across panels, so you are not locked into the messy shape Notion exported. And because notes and files live in the same app, your PDFs and your written notes end up in one searchable, linked place instead of scattered across a documents folder and a separate notes app.

Step 4: Turn pages into editable notes (not just static files)

Markdown files sitting in your vault are safe and searchable, but they are files. If you want to keep editing them as rich notes, with headings, checklists, callouts, links between pages and a graph view, you convert them into Filarr notes.

Filarr ships a notes Import Wizard for exactly this. It walks you through picking a source, selecting the exported folder or ZIP, and choosing options like which notebook to import into, whether to recreate tags, and whether to preserve links between pages. Today the wizard supports Obsidian vaults out of the box. A dedicated Notion importer already lives in the codebase (it reads a Notion ZIP export, cleans those hex UUID suffixes, converts each page's HTML or Markdown into Filarr's editor format, rebuilds your nested page hierarchy into notebooks, resolves links between pages, and even pulls Select and Multi-Select values out of your database CSVs as tags) and it is being finalized before it is switched on in the wizard. Check your version's import screen to see whether the Notion source is live yet.

Until the Notion button is flipped on in your build, you have two honest options that lose nothing:

Keep the pages as Markdown files in the vault (Step 3). They are encrypted, searchable, and openable. This is the zero-risk default.
Import the Markdown folder as a vault of notes. Because a Notion Markdown export is, at bottom, just a folder full of .md files, the notes import path that reads a Markdown directory can ingest them. You will get editable notes, though links written in Notion's URL style will not all reconnect the way native wiki-links do, and you may need to tidy a few filenames by hand. Treat this as the power-user route, not the one-click one.

Whichever you pick, once pages are notes you get the payoff that made Notion appealing in the first place: internal links, backlinks, and a graph view that shows how your notes and files connect, all running locally and all encrypted.

Pitfalls and best practices

Verify before you delete. The cardinal rule. Before you remove anything from Notion, count. Notion's export tells you roughly how many pages you had. After import, check that your note and file counts are in the same ballpark and that a handful of your most important pages actually opened with their attachments intact. Only then consider clearing Notion.

Watch for split exports. Large workspaces come down as multiple ZIPs. It is easy to import ZIP one, feel done, and forget parts two and three. Line them all up before you start.

Attachments are the usual casualty. If you exported without "include files and media", your pages will import with links pointing at Notion URLs that will die the day you cancel your subscription. Re-export with media included rather than trying to patch it later.

Do not expect databases to come alive. Accept that Notion databases arrive as CSV plus per-row pages. Keep the CSVs (they open in any spreadsheet and stay useful), and rebuild only the one or two views you truly rely on. Chasing a perfect database migration is where people burn a weekend and give up.

Write down your recovery phrase. This is not a Notion habit, so it is easy to skip, and skipping it is the one mistake that genuinely loses data. Encryption means there is no "forgot password" email that a support team can send you. Filarr gives you a 24-word BIP-39 recovery phrase. Write it on paper, store it somewhere safe, and treat it like the key to a safe deposit box, because that is exactly what it is.

Migrate in slices if you are nervous. You do not have to move ten thousand pages in one afternoon. Bring over one important area, live in it for a few days, confirm nothing is missing, then move the rest. A staged migration is far less stressful than a big-bang one.

Keep the original ZIP. Even after everything looks good, archive the Notion export ZIP somewhere for a month or two. It costs nothing and it is your ultimate undo button.

Where Filarr is honestly weaker, and where it wins

So you go in clear-eyed: Filarr is younger than Notion and Obsidian. It has fewer third-party plugins than Obsidian's huge ecosystem, its community is newer (2026), and mobile is still in progress. If your workflow depends on a specific Notion integration or a niche Obsidian plugin, check that first.

What it gives you in return is the thing Notion structurally cannot: your files, encrypted per file, on your disk, working fully offline, with notes and documents and a graph in one app. Cloud sync exists but it is optional and it only ever moves opaque encrypted blobs (the server cannot read them), so you are never handing your plain text to anyone. It is free forever locally, and sync starts at 4 euros a month if you ever want your devices to stay in step.

Conclusion: do the safe copy today, polish later

The migration that never loses data is the one you do in the right order. Export everything from Notion with subpages and media included. Look inside the ZIP so you know what you are dealing with. Drop it all into your encrypted vault first, because that alone gives you a complete, private, offline copy. Then, at your own pace, convert the pages you actively work in into editable notes, verify your counts, write down your recovery phrase, and only then clear Notion.

Do the boring, safe copy today. You can always make it pretty next week. What matters is that by tonight your knowledge base can live on your own disk, encrypted, and answerable to no one but you.