What does “PDF to Obsidian” give you?
A plain Markdown file, ready for your vault, that opens as a finished note instead of a pasted PDF.
An Obsidian vault is a folder of Markdown files, so the best thing a PDF can become is one more file in that folder. ocrtomarkdown reads the PDF, scanned or not, joins the broken lines back into paragraphs, puts the headings in order and keeps tables as tables.
The Obsidian format adds one thing the others do not: a properties block at the top of the file, written the way Obsidian expects (a YAML block between two lines of three dashes). It holds the title, the name of the PDF it came from, and the date you converted it.
From PDF to vault in five steps
- Drop your PDF aboveObsidian is already selected on this page.
- Decide about wikilinksLeave the box unticked for a plain note. Tick it if you want “See also” lines and numbered references like [12] turned into [[wikilinks]].
- Check the previewThe Preview tab shows the note the way it will read. The Markdown tab shows the exact text, properties block included.
- Download or copyUse Download .md to get a file, or Copy Markdown to paste into a new note.
- Put it in your vaultDrop the file into your vault folder, or into the Obsidian file list. It appears as a note, and the properties show at the top.
What the properties block looks like
This is the top of an Obsidian note made from a lecture handout:
---
title: "Lecture 4: Cell membranes and transport"
source: "BIOL201-lecture-4.pdf"
date: 2026-10-28
---
# Lecture 4: Cell membranes and transportObsidian reads this block as the note’s properties. The title comes from the first heading in the PDF, or from the file name if the PDF has no heading. The source is the name of the PDF, and the date is the day you converted it. What Obsidian shows as the note’s name is still the file name.
Do not want the block? Delete everything from the first --- line to the second one, and the rest is plain Markdown.
What survives in Obsidian
| In your PDF | In Obsidian |
|---|---|
| Title and headings | One title, then headings in order, down to six levels if the PDF had them. |
| Paragraphs | Joined back together; blank-line breaks stay. |
| Lists | Bulleted and numbered, nested the way the page was. |
| Tables | Markdown tables, which Obsidian shows as tables in reading view. |
| Properties | Title, source and date at the top of the file. |
| Wikilinks | Only if you tick the box: the terms after “See also:” become [[wikilinks]], and [12] becomes [[12]]. |
| Pictures and diagrams | Left out. You get the text and tables around them. |
| Equations | Text equations come through as text. One that could not be read is marked [equation not read]. |
| Page numbers and running headers | Removed when the same line repeats three or more times. |
About the wikilinks option
Obsidian writes links in double square brackets by default, and a link to a note that does not exist yet creates that note when you click it. That is handy for “See also” lines, where each term is often a note you already have or want.
Numbered references are different. [12] becomes [[12]], a link to a note called 12. That suits you if you keep one note per reference. If not, leave the box unticked and your [12] stays as plain text. Existing links, footnotes like [^1] and checkboxes are never touched.
Three ways to get a PDF into Obsidian
| Compared on | Retyping by hand | Generic OCR | ocrtomarkdown |
|---|---|---|---|
| Effort | Copy, paste and rebuild by hand | Convert, then clean up in the note | Drop, check, move into the vault |
| Paragraphs | Rejoined as you go | A line break per printed line | Joined back into paragraphs |
| Properties | Typed by hand | None | Title, source and date added |
| Tables | Rebuilt cell by cell | Rows of loose text | Markdown tables |
| Links to other notes | Added by hand | None | Optional wikilinks for “See also” and [12] |
| Running headers | Skipped | Scattered through the text | Removed |
PDF to Obsidian: your questions
Where do I put the file?
Anywhere inside your vault folder. Save the downloaded .md file there, or drag it into the Obsidian file list. It shows up as a note.
What are the title, source and date lines at the top?
They are note properties. Obsidian keeps properties as a YAML block at the top of the file. Ours holds the title (from the first heading), the name of the PDF, and the date you converted it.
Can I leave the properties out?
Yes. Delete everything from the first --- line to the second one, and what is left is plain Markdown. The block is only added in the Obsidian format.
What does the wikilinks option do, exactly?
It rewrites a line that starts with “See also” so each term becomes a link: “See also: Osmosis; Active transport” turns into “See also: [[Osmosis]], [[Active transport]]”. It also turns numbered references like [12] or [3, 4] into [[12]] or [[3]], [[4]]. It is off unless you tick it.
Will it create a pile of empty notes?
No. Obsidian only creates a note for a wikilink when you open that link. Until then the links are just text in your note.
Does it keep tables?
Yes. Tables are written as Markdown tables with every row padded to the same width, and Obsidian shows them as tables in reading view.
Can I paste instead of saving a file?
Yes. Click Copy Markdown and paste into a new note. Paste the whole thing, including the first lines, so the properties block lands at the very top.
What about scanned handouts?
They work. Scanned pages are read with OCR first. A straight, sharp scan gives the best note.
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.
What does it cost?
3 files a day, up to 10 pages each, are free with no account. Pro is $6 a month for 150 files a month, files up to 150 pages.