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The right Trilium migration route depends on the source format. Import a single Markdown file directly, or put a Markdown folder tree in a ZIP archive. For Obsidian, use Trilium’s dedicated importer with a ZIP of the vault. For Joplin, treat Markdown as a possible interchange route and do not assume that a JEX backup can be loaded directly: the reviewed Trilium documentation does not document JEX import.
Make an untouched copy of the source, test a small representative subset, and inspect the result before importing the full collection. None of these routes should be treated as guaranteed lossless conversions, especially for application-specific metadata, plugins, properties, attachments, and unusual formatting.
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Choose the migration route first
Trilium supports several kinds of import, but the workflows are not interchangeable. This table shows the practical choice for each source.
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| Source collection | Trilium route | Input you prepare | What is documented | Main uncertainty |
|---|---|---|---|---|
| Markdown files | Native Markdown import | One .md file, or a ZIP containing the Markdown tree |
Files and ZIP archives are supported; a directory must be packaged because the browser cannot read a directory directly. Trilium Markdown guide | Note type, attachment paths, and source-specific metadata may need checking. |
| Obsidian vault | Application-specific Obsidian importer | A ZIP of the vault, including folders and resources | Basic Obsidian wikilinks and embedded wikilink images are converted during import. Trilium application import guide | Plugins, properties, advanced embeds, and nonstandard syntax are not promised to transfer identically. |
| Joplin notebook | Conditional Markdown interchange | Markdown export, if your Joplin version provides it, then a file or ZIP suitable for Trilium | Joplin documents JEX as its own backup/re-import format. Trilium’s reviewed native formats are HTML, Markdown, and OPML, and its importer list does not name Joplin. | Direct JEX compatibility and mapping of Joplin tags, resources, geolocation, and other metadata are not established. |
Trilium says that “Starting with version v0.104.0, Trilium’s importer was expanded to application-specific imports.” Check the version you are running before looking for the Obsidian-specific workflow; labels and availability can vary by release.
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Prepare a safe test migration
Migration changes how your notes are represented. Preserve the original before you export, convert, rename, or delete anything.
- Make an untouched source copy. Duplicate the Markdown directory, Obsidian vault, or Joplin data/export on separate storage. Keep this copy unchanged until you have verified the Trilium result.
- Select a representative sample. Include nested folders, internal links, images, file attachments, tags or properties, long notes, tables, code blocks, and any unusual formatting. A sample containing only plain paragraphs will not reveal the difficult cases.
- Keep the archive root predictable. When creating a ZIP, include the vault or note tree and its resource folders in a stable relative layout. Do not flatten folders merely to make the archive smaller; relative paths are important for links and attachments.
- Record what must survive. Make a short checklist of notes, hierarchy, links, images, attachments, tags, properties, dates, and any source-app features you rely on. You will use it during validation.
- Import the sample first. Resolve broken paths, unexpected note types, and missing metadata before processing the complete collection.
A browser-based import cannot read a directory as a directory. That is why Trilium’s Markdown instructions require a ZIP for a whole tree rather than asking the browser to select a folder.
Migrate Markdown files
Import one Markdown file
Use this route when you have a single note or want to test one file.
- Open the Trilium note where the imported item should be placed.
- Choose the import command from the note controls. Depending on the interface, this is exposed as Import into note or through the import/files controls.
- Select the
.mdfile and confirm the import. - Open the resulting note and check headings, lists, code blocks, tables, links, images, and any relative attachment references.
By default, a single imported Markdown file is converted to a Trilium Text note. If you need the source to remain an editable Markdown note, use Import into note and clear the option labeled Import HTML, Markdown and TXT as text notes when it is shown. The Markdown note type and its attachment-link behavior are described in Trilium’s Markdown note documentation.
Import a folder tree as a ZIP
- Close or pause applications that may be rewriting the source files while you archive them.
- Create a ZIP containing the Markdown files and the folders that hold their images or other attachments. Preserve the relative paths used by the notes.
- In Trilium, open the import dialog from the Note Tree or the note buttons area and select the ZIP. You can also drop an archive into the Note Tree when your build supports archive detection.
- Choose the destination parent note and start the import.
- Wait for the import to finish before opening many notes at once, especially for a large archive.
- Inspect the sample hierarchy and several notes before importing the full tree.
Trilium’s archive import can rewrite attachment links as relative paths and rewrite them back during import in the documented Markdown workflow. That behavior is useful for Trilium’s supported interchange format, but it does not prove that every external Markdown generator uses paths Trilium can resolve automatically.
Decide whether the result should be Text or Markdown notes
Text notes are generally convenient when you want Trilium to render and edit the imported content as rich note content. Markdown notes are preferable when retaining Markdown source semantics is important and you expect to continue editing the source-style syntax. Make this decision during the sample import, because changing note types later can alter how formatting and attachments are handled.
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Check Markdown syntax and paths
Trilium’s supported-syntax documentation follows GitHub-Flavored Markdown as its main syntax. Standard headings, lists, tables, fenced code, and ordinary links are the safest cases. Check source features that depend on a particular editor, such as custom callouts, plugin directives, transclusions, special front matter, or application-only embeds. Review the supported syntax list before assuming a visual match.
For each sample note, test links rather than judging only the rendered page:
- Open links to another imported note and confirm they reach the intended destination.
- Open every image and a few non-image attachments.
- Look for literal path text, missing-image icons, or links that still point to the old absolute location.
- Compare a note in a nested folder with one at the archive root; relative-path errors often appear only at one depth.
Migrate an Obsidian vault
Prepare the vault ZIP
Use Trilium’s application-specific Obsidian importer rather than treating the vault as an arbitrary Markdown folder. Create a ZIP of the vault that includes its note folders and the attachment/resource folders referenced by those notes. Keep the directory relationships intact. If your vault contains files that are not needed, you can omit them from a test archive, but do not omit resources required by the sample notes.
The importer’s documented input is a ZIP of the vault. Trilium’s general import guide also says that dropping an archive into the Note Tree can automatically detect some formats, including Obsidian. The explicit Obsidian importer is the safer choice when you want to verify that the application-specific path was selected.
Run the Obsidian import
- Open the Trilium import dialog from the Note Tree or the note buttons area.
- Select the application-specific Obsidian option, or use the documented archive-drop detection if that is how your release exposes it.
- Choose the ZIP of the vault and set the destination parent note.
- Start the import and allow the archive to finish processing.
- Open representative notes from the root and from several nested folders.
If you cannot find the Obsidian option, verify that the installed Trilium version includes the application-specific importer introduced in v0.104.0. Do not infer that a missing menu item means the vault itself is invalid.
Understand wikilink conversion
Trilium documents basic Obsidian-style wikilinks such as [[folder/note]] and embedded wikilink images such as ![[folder/image.png]]. During import, link paths are resolved relative to the archive’s import root and converted to Trilium-compatible syntax. Test both a link to a note and an embedded image in a nested folder, because a root-level example alone does not verify path resolution.
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The documented wikilink support is import-only. It does not mean that Trilium and Obsidian will continue to maintain identical wikilink syntax after the import, nor does it guarantee conversion of every plugin-generated link, block reference, transclusion, or custom embed.
Inspect features beyond basic Markdown
Obsidian vaults commonly contain more than Markdown text. Treat the following as verification points rather than promised conversions:
- Front-matter properties and newer property types.
- Community-plugin fields, scripts, tasks, and custom callouts.
- Canvas files, block references, transclusions, and embeds that are not ordinary Markdown or basic wikilinks.
- Renamed files whose old paths still appear in links.
- Attachments stored outside the note folder or referenced through aliases.
Open the source and imported versions side by side for these cases. If an important feature becomes plain text or disappears, retain the original vault and decide whether to recreate that information in Trilium manually.
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Why a JEX file is not a documented direct route
Joplin describes JEX as a tar-based export and backup format intended for re-importing into Joplin, including Joplin metadata such as tags and geolocation. See Joplin’s importing and exporting documentation.
The reviewed Trilium documentation lists native HTML, Markdown, and OPML formats and names application-specific importers for other applications, but does not list Joplin. Consequently, you should not select a JEX file in Trilium expecting a supported Joplin migration. Direct JEX compatibility, and preservation of Joplin-specific metadata through such a path, are not established.
Use Markdown only as a conditional interchange format
Markdown is the most plausible bridge because Trilium has native Markdown import. However, the available Joplin documentation does not establish one universal Markdown-export sequence for every Joplin version, nor does it specify how all Joplin metadata maps into Trilium.
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- In your installed Joplin version, look for the current export command and determine whether it offers Markdown. Menu names can change between desktop and mobile releases.
- If Markdown export is available, export a small notebook first. Choose the export variant that includes the associated resources when Joplin presents such a choice.
- Preserve the resulting folder relationships and attachment files. Do not move images into a different directory before testing.
- Package the exported Markdown tree as a ZIP if you are importing more than one file into Trilium.
- Run the Markdown workflow described above and compare tags, dates, resources, links, and formatting with the Joplin originals.
Do not describe this as a verified, lossless Joplin-to-Trilium converter. Markdown can carry note content and ordinary links, but Joplin’s tags, geolocation, notebook metadata, resource records, alarms, and other application data may require separate handling. If a field matters, record it before migration and check whether it appears in the imported note or must be recreated.
Validate the imported collection
Validation is the point at which a trial import becomes a safe migration plan. Use a checklist rather than opening only the first few notes.
Content and formatting
- Compare headings, lists, tables, inline formatting, code blocks, checkboxes, and non-ASCII characters.
- Open long notes and notes with unusual formatting; truncation and unsupported syntax may not be visible in short examples.
- Check whether the chosen Text or Markdown note type matches the editing workflow you want.
Hierarchy and note identity
- Confirm that top-level folders and deeply nested folders are present.
- Check notes with identical names in different folders to ensure they remain distinguishable.
- Compare the number of sample notes with the source subset and look for skipped or duplicated files.
Links, images, and attachments
- Follow internal links in both directions where applicable.
- Open images, PDFs, audio, and other attached files rather than checking only that a filename appears.
- Search for old absolute paths, unresolved relative paths, and literal wikilink text.
- Test resources located beside a note and resources located in a shared attachment folder.
Metadata and application features
- Check tags, properties, creation or modification dates, geolocation, and other fields that your source application stored.
- For Obsidian, test plugin-generated content and advanced embeds separately from basic wikilinks.
- For Joplin, compare the metadata you explicitly marked as important; do not assume that a Markdown export contains JEX’s metadata.
Trilium notes can contain both content and children, so the note tree can represent hierarchy as well as document content. That model does not establish that every source application’s folder, notebook, or metadata structure will map exactly. Trilium’s notes documentation explains the underlying model.
Size, memory, and version considerations
Trilium’s general import documentation states that a single imported item is limited to approximately 374 MiB, with the limit determined by the synchronization protocol. This is a per-item operational limit, not a stated maximum for the total collection.
For a large desktop import, use the import dialog rather than assuming the browser must upload the entire archive again. Trilium 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 product-documentation operational figures, not a guarantee of migration speed, capacity, or fidelity on your computer. Read the current Import & Export guide and leave adequate free disk space and memory.
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Troubleshoot common migration failures
The import menu does not show Obsidian
Confirm the Trilium version and look in both the Note Tree and note buttons area for import commands. Application-specific importers are described as beginning with v0.104.0. If the feature is absent in your build, do not pretend that renaming the ZIP or using JEX will activate it; use the documented Markdown route only after checking what your installation supports.
The browser will not let me choose a folder
That is expected for the browser-based directory restriction described in Trilium’s Markdown guide. Compress the folder tree into a ZIP and import the archive instead.
Images or attachments are missing
Recreate the test archive with the resource folders included and the same relative paths used by the notes. Inspect one missing file’s source path and compare it with the path inside the ZIP. Do not move attachments after export until you know how the importer resolves them.
Links appear as plain text or point to the wrong note
Check whether the source used basic Markdown links, supported Obsidian wikilinks, or an application-specific syntax. For Obsidian, verify that the note and target are both inside the same archive root and that the target path matches the documented basic wikilink form. Plugin links and advanced references may require manual replacement.
JEX is rejected
A rejection is consistent with the absence of documented JEX support in Trilium. Return to the original Joplin data, create a conditional Markdown export if your Joplin version offers one, and test the resulting files and metadata separately. Keep the JEX backup as a Joplin recovery copy.
The result contains duplicate notes
Stop the full migration and compare the destination tree with your import log. Duplicates usually become harder to identify after several retries. Delete only duplicates you can positively identify, then rerun a clearly labeled archive into a clean destination or a new test branch.
A practical decision checklist
- Markdown source: one file can be imported directly; a collection should be ZIP-packaged.
- Obsidian source: ZIP the complete vault and use the dedicated Obsidian importer when available.
- Joplin source: keep JEX for Joplin backup/re-import and use Markdown only as a conditional bridge.
- All sources: preserve an untouched copy, import a representative sample, and verify hierarchy, content, links, attachments, and important metadata.
- Large jobs: respect the approximately 374 MiB single-item figure, use the desktop import dialog where appropriate, and plan for substantial memory use.
Once the sample passes your checklist, repeat the same route for the full collection in labeled batches. Keep the original source until you have completed a second review and have a backup of the resulting Trilium data.
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