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The correct Trilium migration route depends on your source: import a single Markdown file or a ZIP of a Markdown tree with Trilium’s native Markdown importer; import an Obsidian vault as a ZIP through Trilium’s Obsidian-specific importer; and treat Joplin’s JEX file as a Joplin backup, not as a format that Trilium’s documented importers accept directly.
Make an untouched copy of your source, test a representative subset, and inspect links, attachments, hierarchy, formatting, and metadata before importing the rest. None of these routes should be assumed to be perfectly lossless.
Choose the route before you export anything
| Source collection | Trilium route | Input | What the documentation establishes | Main uncertainty |
|---|---|---|---|---|
| Markdown files | Native Markdown import | One .md file, or a ZIP containing the folder tree |
Trilium accepts an individual Markdown file and a collection packaged as a ZIP. A browser cannot supply a directory directly to the importer. | Formatting extensions, attachment paths, and source-specific metadata may need checking. |
| Obsidian vault | Application-specific Obsidian importer | A ZIP of the complete vault, including note folders and attachments | Basic Obsidian wikilinks and embedded wikilink images can be converted, with paths resolved relative to the import root. | Plugins, advanced embeds, properties, and other Obsidian-only features are not guaranteed to map identically. |
| Joplin collection | Markdown interchange, only if your Joplin version offers a suitable Markdown export | Markdown files and resources produced by the export you select | Trilium’s documented native formats include HTML, Markdown, and OPML; its listed application-specific importers do not include Joplin. | Direct JEX import is not established, and Joplin tags, notebooks, IDs, geolocation, and other metadata may not have a one-to-one destination. |
Trilium’s guide says, “Starting with version v0.104.0, Trilium’s importer was expanded to application-specific imports.” That version context matters for the Obsidian workflow; confirm the installed Trilium build before looking for an application-specific option. See Trilium’s application-import guide.
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Migration changes how files, links, resources, and metadata are represented. Preserve the original collection before you rename files, run a converter, or export from the source application. Keep that copy read-only until you have verified the Trilium result.
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1. Make a representative test set
Do not test only a plain text note. Select a small subset that contains:
- Several levels of nested folders or notebooks.
- Internal links, backlinks, and links whose targets have similar names.
- Images, PDFs, other attachments, and files stored in resource folders.
- Tags, properties, front matter, tables, checklists, code blocks, and unusual formatting.
- At least one long note and one note with a non-ASCII filename or characters.
A sample exposes path and conversion problems while the source is still intact. It is a practical safeguard, not a Trilium requirement.
2. Record what “successful” means for your collection
Before importing, decide which information must survive: readable content, editable Markdown, folder hierarchy, internal links, images, attachments, tags, dates, task state, or application-specific properties. A conversion can preserve the words while losing a property or changing a link target, so define acceptance criteria instead of relying on a visual spot check.
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Trilium documents a maximum size of approximately 374 MiB for one imported item, determined by its synchronization protocol. This is a per-item figure, not a limit on the total number of notes. For large desktop imports, the import dialog reads from disk rather than uploading the item again; use that dialog instead of treating a very large archive as a browser upload. Trilium also documents that large imports and exports can use around 2 GB of memory and reports a test involving a 2.4 GB database with approximately 21,000 notes. Those are operational figures from the product documentation, not a promise that every computer will handle the same workload.
Import a single Markdown file or a Markdown folder tree
Use this route for ordinary Markdown collections and for a Joplin export that you have deliberately converted to Markdown. Trilium’s native Markdown instructions are at the Markdown import and export guide.
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One .md file
- Open the destination location in Trilium’s Note Tree.
- Open the import command from the Note Tree or the Note buttons area and choose the Markdown file.
- Review the note type option before confirming the import.
- Open the resulting note and check headings, lists, code, links, images, and any front matter or extensions.
By default, a single imported Markdown file is converted to a Trilium Text note. If you want to keep an editable Markdown source note instead, use Import into note and, when the option appears, uncheck Import HTML, Markdown and TXT as text notes. The note-type behavior and attachment-link details are described in Trilium’s Markdown note documentation.
A collection of Markdown files
- Copy the complete Markdown tree and its resource folders into a staging directory.
- Create a ZIP archive that retains the relative folder paths and all attachments required by the notes.
- In Trilium, open the import dialog and select the ZIP, or drop the archive into the Note Tree if your version supports automatic archive detection.
- Choose the destination parent note and complete the import.
- Expand several branches in the Note Tree and open notes at different depths before importing the full archive.
Trilium’s browser-based importer needs the directory packaged because a browser cannot read a local directory as a single import item. The ZIP should therefore contain the tree you want represented, rather than only a random selection of files. The Import & Export guide describes archive detection and supported formats.
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For Trilium’s own Markdown ZIP workflow, attachment links can be rewritten to relative paths and rewritten back during import. That documented behavior should not be treated as a guarantee for every external Markdown exporter. Inspect an image, a downloadable attachment, and at least one internal link whose target is in another folder. A link that looks correct in Markdown can still point to the wrong note after the folder tree is inserted under a new parent.
Import an Obsidian vault
Use Trilium’s dedicated Obsidian route rather than treating the vault as an undifferentiated folder of Markdown files. The application-specific importer takes a ZIP of the vault. The general import documentation says that dropping an archive into the Note Tree can automatically detect some formats, including Obsidian; the application-import guide describes the Obsidian option under Import into note or Import files.
Create the vault ZIP
- Close editing sessions or sync activity that could change files while you are packaging them.
- Include the vault’s Markdown notes, nested folders, and attachment directories in one archive.
- Keep relative paths unchanged. Do not flatten folders or rename files solely to make the ZIP smaller.
- Exclude caches or temporary files only when you know they are not referenced by notes; retain anything that is an actual attachment or source note.
Obsidian’s own documentation also describes importing Markdown files and folders; see Obsidian’s Markdown import page for the source-side context. The archive you give Trilium should represent the vault you intend to migrate, not a partial export that omits resources.
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Run the Obsidian importer
- In Trilium, select the parent note where the vault should appear.
- Open Import into note or Import files, then choose the Obsidian importer if it is listed.
- Select the vault ZIP. If your build supports automatic detection, dropping the archive into the Note Tree may select the same importer.
- Wait for the import to finish before moving or renaming imported branches.
- Open notes from several folders and test both an internal link and an embedded image.
How wikilinks are handled
Trilium documents basic Obsidian-style links such as [[folder/note]] and embedded wikilink images such as ![[folder/image.png]]. During import, paths are resolved relative to the archive’s import root and the wikilinks are changed into Trilium-compatible syntax. The documented wikilink support is import-only; it does not mean that Trilium and Obsidian will continue to share the same source syntax after migration. See Trilium’s supported-syntax guide.
Test links that use folders, duplicate note names, URL-encoded characters, headings, or block references separately. The basic documented cases do not establish support for every Obsidian plugin, advanced embed type, property format, canvas, or extension. Plan to clean up those features in Trilium rather than assuming they will transfer unchanged.
Move a Joplin collection without treating JEX as a Trilium format
Joplin’s JEX file is documented as a Joplin export and backup format intended for re-importing into Joplin. It is a tar-based package that can preserve Joplin metadata such as tags and geolocation. Trilium’s documented native formats are HTML, Markdown, and OPML, and the application-specific importer list names services such as Obsidian, OneNote, Notion, Google Keep, Evernote, and Anytype—not Joplin. Therefore, do not upload a .jex file to Trilium expecting a supported direct import.
Joplin’s import/export help is available at Joplin’s official import and export page. That page documents JEX export and Markdown import, but it does not establish a universal Markdown-export sequence for every Joplin version or explain how Joplin-specific metadata maps into Trilium.
If your Joplin version offers Markdown export
- Keep the original Joplin profile and a JEX backup untouched.
- Use the export menu in your installed Joplin version to create Markdown files and include resources if that option is offered.
- Open the exported files outside Trilium and verify that notes, resource files, and relative paths are present.
- Package the resulting Markdown tree as a ZIP, preserving its directories.
- Import that ZIP through Trilium’s native Markdown route.
- Compare tags, notebook hierarchy, dates, task state, attachments, and representative links against the original Joplin notes.
The exact menu labels and available export choices can vary by Joplin release, so follow the labels shown by your installation. If your version does not provide a usable Markdown export, do not rename a JEX file to .zip or .md; that changes the extension, not the file format. Use a documented export option or an intermediate conversion tool only after checking what it preserves.
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What may not map cleanly
Markdown can carry the note body and some links, but it is not a complete representation of every Joplin feature. Treat tags, notebook IDs, geolocation, creation and update dates, task metadata, and resource relationships as items to verify. If a particular Joplin property is essential, record it before conversion or retain Joplin as an archive until you have confirmed an equivalent Trilium representation.
Validate the imported tree before replacing the source
Trilium notes can contain content and children, allowing a note tree to represent both document text and hierarchy. That model does not establish that an external application’s notebooks, folders, or saved searches will always map exactly. The Trilium Notes guide explains the note-tree model.
Content and formatting checklist
- Open short, long, and deeply nested notes.
- Check headings, tables, lists, checkboxes, block quotes, code blocks, footnotes, and inline HTML.
- Look for literal Markdown markers where rendered content was expected, and for formatting that disappeared.
- Check non-ASCII text, emoji, dates, and filenames.
Hierarchy and identity checklist
- Expand every level of the imported branch and compare counts with the source subset.
- Check duplicate filenames and notes with the same title in different folders.
- Confirm that the intended parent-child relationships exist rather than merely appearing as a flat list.
- Verify that archived, deleted, or excluded source folders were not accidentally included.
Links and resources checklist
- Open an internal link to a note in the same folder and one in a different folder.
- Test an image embedded in a note and an attachment opened as a file.
- Inspect links containing spaces, Unicode characters, relative paths, or duplicate basenames.
- Search for broken-link indicators or unresolved text left by the importer.
Metadata checklist
- Compare tags and important properties on several notes.
- Check created and modified dates if your workflow depends on them.
- Review task completion state, aliases, front matter, and source-specific fields.
- Keep the original source until the metadata review is complete.
Troubleshoot the common failure modes
The importer does not appear
Application-specific importers are described from Trilium v0.104.0 onward. Check the installed version and update only after preserving your source. If the Obsidian option is absent, use the documented native Markdown route as a fallback, understanding that it will not provide the same application-specific wikilink handling.
The ZIP imports as one unexpected note
Confirm that you selected the archive import command and that the ZIP contains the intended folder tree rather than another nested ZIP. Try the import dialog instead of dragging the file, particularly for a large archive. Open the archive outside Trilium to confirm that attachments and relative paths are present.
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Images or attachments are missing
Check whether the source export included resource files and whether their relative paths still match the Markdown references. Rebuild the archive with the attachment directories included. A successful note-body import does not prove that external resources were packaged.
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Links are plain text or point to the wrong note
For Obsidian, check that links use one of the basic documented wikilink forms and that the referenced path is inside the archive’s import root. For ordinary Markdown, inspect relative paths after the tree has been placed under its Trilium parent. Duplicate names and unsupported advanced syntax may require manual relinking.
Large imports stop or the browser becomes unresponsive
Split the collection into smaller testable archives, use Trilium’s disk-reading import dialog for desktop imports, and stay within the approximately 374 MiB single-item figure documented by Trilium. Monitor available memory; the guide notes that large operations can use around 2 GB. Do not infer from those figures that a particular computer is guaranteed to complete a multi-gigabyte migration.
A practical order of operations
- Preserve the original Markdown tree, Obsidian vault, or Joplin profile and JEX backup.
- Choose the source-specific route in the comparison table.
- Create a small subset containing nested structure, links, resources, formatting, and metadata.
- Import the subset and run the validation checklists.
- Adjust the export, archive layout, or note-type setting if the result is wrong.
- Import the remaining collection in manageable archives.
- Recheck representative branches and keep the source copy until the migration is accepted.
This sequence separates format conversion from data verification: Trilium can receive the files, but only inspection can tell you whether the information that matters to your workflow survived.
Frequently Asked Questions
Can I import a JEX file directly into Trilium?
Not on the basis of Trilium’s documented formats. JEX is documented as Joplin’s own backup and re-import format; use a suitable Markdown export instead and validate what metadata it preserves.
Does Trilium preserve every Obsidian plugin and property?
No complete preservation is established. Trilium documents basic wikilinks and embedded wikilink images, so inspect advanced embeds, plugins, properties, and other Obsidian-specific features individually.
Why must a Markdown folder be zipped first?
The browser-based importer cannot read a directory directly as one item. Packaging the tree as a ZIP preserves its relative paths for Trilium’s archive import.
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