March 18, 2025, 8:46pm 1

I’m new to Obsidian and Notesnook and trying to figure out the best way to structure my notes securely. I want to use one (or both) of these tools, but I have some concerns about security, usability, and workflows.

My Use Case

• I want to store personal notes, ideas, and task/project management (possibly GTD style).
• Security and privacy are important to me, so I’m leaning towards Notesnook’s E2EE.
• I like the idea of local-first control with Obsidian, but I’m concerned about security since it doesn’t have built-in E2EE.
• I want cross-device sync but don’t want my data exposed to cloud risks.

My Questions

1. Security Concern: Since Obsidian is not E2E encrypted, how do people securely store personal/private data in it? Would using Cryptomator, Syncthing, or other encryption tools help?
2. Use Both? Should I use Obsidian for knowledge management (Zettelkasten, GTD, etc.) and Notesnook for sensitive private notes?
3. Syncing & Privacy: If I self-host sync with Obsidian Sync, iCloud, or Syncthing, does that make it private enough?
4. Proton Drive & Encryption: Can I store my Obsidian vault in Proton Drive for encryption? Would this be secure enough, or should I use Cryptomator + Proton Drive instead?
5. Workflow Suggestions: If you use both, how do you split them up?

I’d love to hear how you all handle privacy, syncing, and note organization between these two apps. Any best practices or security tips would be super helpful.

2 Likes

yes it would. Definitely use that wherever you can.

I recommend Notesnook unless there’s something particular about the other you find compelling enough to not let go. There’s still a lot you can do with Notesnook.

It could - but security is more of a question here than privacy. You’ll have to ensure of privacy too.

Yes this option. Proton Drive will be much too slow for backup and everyday usage.

This would depend on what kind of work and projects you have to manage and how you want to go about them. This is a personal question and would depend on how they want to do it. No right or wrong answer here. But I would choose Notesnook. It feels like a much simpler solution for all that it can do.

Obsidian has paid cloud syncing that is e2ee. If you go the local route and your disk is encrypted (FileVault, LUKS, Veracrypt, Bitlocker for desktop and smartphones are encrypted anyway) you don’t have to worry.

Well Proton Drive is e2ee. You can trust Proton in my opinion so there is no need to use Cryptomator before uploading to Proton Drive.

Not sure about what do you mean. Yes you can use Obsidian Sync and it’s probably great. Yes you can also use Obsidian locally and sync with iCloud. In this case, turn Advanced Data Protection on in your iCloud account, or use Cryptomator before uploading to iCloud. Yes you can also use Syncthing but this is a very different set-up. Syncthing is not cloud storage like Obsidian Sync or iCloud.

Wanting to use the Zettelkasten method is what made me choose Obsidian as my main app. It has a built-in function to auto-generate a unique id for notes, and it is excellent at cross-note linking.

Also, the free version far more comprehensive than the free version of alternative apps.

To keep things private, I only use it offline on my device. I use syncthing to sync my desktop PC notes with my laptop notes (by folder), and I use Vorta (on Linux) to make backups to both a local external drive and also BorgBase for an offsite backup. Vorta lets you encrypt your backup before it leaves your device, so anything stored anywhere else is encrypted, whether it’s a local device or a server further away.

When I say backup here, I don’t mean having another ‘copy’ which is what syncthing does. I’m referring to incremental backups which record changes over time and only save the changes, so you have incremental copies of your files at different points in time.

Obsidian has a remotely-save plugin via which you can do e2ee before uploading to a cloud service. If you don’t want anything to leave your device, use syncthing. If you don’t like using any plugins, iCloud is okay, and you could encrypt before uploading. Self-hosting Obsidian Sync is also a nice option. Notesnook is safe since e2ee is default, so if you have any sensitive information that you don’t want to leave as clear text, go with that. Obsidian is probably the greatest markdown editor in history and far more functional than any other, so I’m not saying anything like Logseq or Joplin as substitute. Because I used all of them for a long enough period of time and I believe that it’s misleading to address Logseq and Joplin as “open source replacement of Obsidian”.

micdan (Michael) March 25, 2025, 2:04am 6

I’ve been using Obsidian since January and it’s just amazing. It has community-made extensions, which I don’t like much because some of them may slow down Obsidian or some of them may be outdated, but I’m just able to get hundreds of notes organized and even do some HTML formatting natively without any extensions.

I have used both and I always fell like I can do more with Notesnook. It’s a no-nonsense app. You install it and start doing your work. Also more intuitive than Obsidian imo. The only gripe I have with it is Sync which is not very reliable some times. Maybe an issue with my internet but who know. Also, I think you can disable sync in the settings so you will have encrypted data in your local disk but make sure you don’t uninstall the app or your data will be gone as it’s not syncing. You should give it a try

2 Likes

micdan (Michael) March 25, 2025, 4:30pm 8

I have a question: I never tried Notesnook before. Could I sync my data locally? Like storing my content locally and sync it with Syncthing.

I am not sure about Syncthing as I have never tried that for Notesnook. However, you can use it locally. Just disable the sync in settings. As for syncing with Syncthing, you can ask on their discord channel. The discord community is very active.

1 Like

This is something I’m VERY interested in. I’m trying to move away from all these cloud services and rely on myself by creating self-hosting solutions at home that are all disconnected from the cloud.

EDIT: Did you think about using Veracrypt and creating Veracrypt containers and then storing them locally?

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I have not considered using veracrypt. I have a Mac, so I use FileVault. I think I’ve decided to use Notesnook. The down side with Obsidian is that it is not open source and you have to use Obsidian Sync for E2EE. The pro to Obsidian is that it is highly customizable. I really like the mindmap for Obsidian but have found that I can practicaly do the same function by linking notes to each other. Overall, the trajectory of Notesnook seems stronger, they have a great community, and they are exactly what I was looking for in a notes application to serve as my second brain.

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What of these privacy-friendly notetaking apps support page tree hierarchy? Like Confluence or Notion.

• Page

• Subpage

• Subsubpage

• Subsubsubpage

• Page

In Notesnook, you can oranize by Notebook > subnotebook > Subsubnotebook, etc. I’m not sure how many levels you can do. The main link between notes themselves are bi-directional note links, which I’ve found to be very useful.

1 Like

Average_Joe (Joey) November 10, 2025, 8:31am 14

I appreciate your reply!

Just be careful of relying on Filevault. Have you looked at Veracrypt or Picocrypt-NG: GitHub - Picocrypt-NG/Picocrypt-NG: A very small, very simple, yet very secure encryption tool.