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Joplin can encrypt and it is selfhostable and uses Markdown
Benefit: apps for every platform
After some more research it seems that Joplin only E2E encrypts notes at transport and not at rest[1]? e.g. it only stores plain text files on the harddrive just like Obsidian does? This sadly makes it not viable for my use case :/
[1] https://discourse.joplinapp.org/t/requesting-encryption-of-local-joplin-data-at-rest-encryption/15145
They do encryption at rest too. Really good notes app and it's cross platform too. Only missing a “web” client for when you want to access your notes on a computer without Joplin installed (but that defeats the purpose of the E2EE IMO)