Import PDF notes into Obsidian with properties and links sorted
Convert the PDF to an Obsidian-format Markdown file, rename it, and drop it into a folder in your vault. It opens as a note with title, source and date as properties. Rename first: Obsidian names the note after the file, not after the title property.
What Obsidian does with a Markdown file
An Obsidian vault is an ordinary folder of Markdown files, so importing is really filing. Obsidian’s Importer plugin lists apps such as Notion, Evernote, OneNote and Apple Notes, plus HTML, CSV, Markdown and Textbundle files. Its help page does not list PDF, which is why a PDF first needs turning into Markdown.
Three things then decide how tidy the result is: the file name, the properties block at the top of the file, and where the original PDF lives. A useful habit is an Inbox folder for fresh conversions, so you can read each note against its PDF before it joins the rest of the vault.
Headings matter more than they look. Obsidian’s search has a section: operator that finds matches in the same section, meaning the text between two headings. A note with clear headings is easier to search that way. Headings that make notes searchable explains the rules.
Bring a PDF into your vault in six steps
- Choose a home for itPick a folder, such as one per course or project, or an Inbox for review. Folders are for your own tidiness; the note works wherever it sits.
- Convert with the Obsidian formatOn PDF to Obsidian pick Obsidian in step 2. Leave wikilinks off unless you want “See also” lines and numbered references turned into links.
- Rename the fileObsidian names the note after its file. Use a short, unique name, and avoid # | ^ : %% [[ ]], which Obsidian’s help page says may not work in links and recommends keeping out of file names.
- Put it in the vaultDrop the .md file into the folder, or paste the copied text into a new note. If you paste, the first line must be the three dashes: the help page says properties start at the very beginning of the file.
- Check the propertiesOpen the note. Title, source and date show as properties. The date is the day you converted, not the document’s date. Add tags or aliases if you use them.
- Keep the original PDF beside itSet a default location for new attachments, then drag the PDF in and embed it, as the example below shows. Pictures are not in the converted note, so the PDF is where they stay.
The top of a note, with the PDF embedded
This is the converter’s properties block, then an embed line you add yourself.
---
title: "Lecture 4: Cell membranes and transport"
source: "BIOL201-lecture-4.pdf"
date: 2026-10-28
---
![[BIOL201-lecture-4.pdf#page=3&height=400]]
# Lecture 4: Cell membranes and transportObsidian’s help page gives the embed forms ![[file.pdf]], #page=3 and #height=400, and says to join two with &. Pictures stay in the PDF, so this keeps diagrams one click from the note.
The parts of an imported PDF note
Read across each row: the middle column is what the converter hands you, and the last is what is left for you to decide in the vault.
| Part | What the converter gives you | What to do in Obsidian |
|---|---|---|
| Folder | One .md file | Drop it into any vault folder. The layout is yours. |
| Note name | The file name you give it | Rename it first, without # | ^ : %% [[ ]]. |
| Properties | title, source and date in a YAML block | Add tags or aliases if you use them. Put link values in quotes. |
| Wikilinks | Off unless you tick the box | When ticked, “See also” terms and [12] become links. A link makes a note only when you open it. |
| Pictures | Left out | Keep the original PDF in the vault and embed it. |
| Attachments | None | New attachments go to the vault root unless you change the setting. |
What goes wrong when you import
The properties show as text
The three dashes are not on the first line, often because a blank line or a heading sits above them after a paste. Move them to the very top of the file and the block turns into properties.
The note has the wrong name
Obsidian shows the file name, and the title property is only metadata. Rename the file, not the property.
Empty notes pile up
A wikilink such as [[12]] points to a note called 12, and Obsidian creates that note when you open the link. Leave wikilinks off unless you really keep one note per reference.
Attachments land in the root
Obsidian’s help page says new attachments go to the vault root by default. Change Default location for new attachments before you add many.
Two notes share a name
Chapter 1 from two books can make short links ambiguous, and it is hard to tell the two apart in the file list. Put the course or book in the file name.
A diagram is missing
Pictures are left out of the note. Embed the PDF page with ![[file.pdf#page=3]] and read the diagram there.
How ocrtomarkdown helps
The Obsidian format writes the properties block for you, with the title from the first heading, the PDF’s name as the source and the day you converted. It joins broken lines into paragraphs, keeps headings in order and tables as tables, and adds wikilinks only if you ask. Convert on PDF to Obsidian. Free: 3 files a day, up to 10 pages each, no account. Files over 10 pages are converted up to page 10 on the free allowance; a page code converts the whole file, up to 150 pages. See pricing.
PDF notes in Obsidian: your questions
Where do I put the converted file?
Anywhere inside your vault folder. Save the .md file there or drag it into the file list, and it appears as a note.
Can Obsidian import a PDF as a note itself?
Obsidian’s Importer help page lists apps plus HTML, CSV, Markdown and Textbundle files, and not PDF. Convert the PDF to Markdown first.
Can I delete the properties block?
Yes. Delete everything from the first --- line to the second, and the rest is plain Markdown. It is only added in the Obsidian format.
Does the title property rename my note?
No. Obsidian shows the file name as the note name. The title property is metadata taken from the first heading.
Should I turn on wikilinks?
Only if you want “See also” terms and numbered references as links. Otherwise leave them off, so [12] stays plain text.
How do I keep the original PDF with the note?
Drag the PDF into the vault and embed it with ![[file.pdf]]. Add #page=3 to open at a page, and #height=400 to set the height.
Where does Obsidian save attachments?
By default in the vault root, according to its help page. Settings, then Files & Links, then Default location for new attachments changes that.
Can I convert a folder of PDFs?
One file at a time for now. Batches of up to 12 files are planned for Pro and are marked as coming soon.