How I Write My Dissertation in Obsidian (Without Losing My Mind)

29 June 2026 - 5 mins read time
Tags: obsidian academic-writing zotero pandoc research

Word plus Zotero is where most students start, and it works, until it doesn’t. The moment your bibliography hits 150 sources, your argument spans five chapters, and you need to cross-reference figures three sections back, the cracks show: citations feel bolted on (because they are), there’s no connection between your reading notes and your writing, and every export is a negotiation with an uncooperative .docx or losing your mind trying to use raw LaTeX. The alternative is treating Obsidian as the actual writing environment, not just a note-taking app parked next to Word, but the place where literature notes, drafts, citations, and final output all live together.

Here’s the full pipeline.

The pipeline

Search for sources (Google Scholar, SciHub)
Import to Zotero via browser extension
Annotate PDFs in Zotero
Export highlights to literature notes in Obsidian
Write manuscript with inline citations
Export via Pandoc to PDF, Word, or LaTeX

Reading feeds notes. Notes feed writing. Writing exports. Nothing needs to move between apps.

Setting up Zotero

Install the Zotero browser extension first. It pulls paper metadata from any journal page directly into your library with one click, no manual entry.

Then install two Zotero plugins:

Zotfile handles PDF management and annotation extraction. Read papers on a tablet and the annotations sync back into Zotero automatically.
BetterBibtex generates persistent, human-readable cite keys (e.g. smith2021agency) and keeps your .bib file current.

Export your library as a .bib file: go to File → Export Library, choose BibLaTeX format, enable Keep Updated and Export Notes, and set the automatic export trigger to On Change. Every paper you import from this point on shows up in the file without any manual steps.

Gotcha: File paths with spaces will break pandoc arguments later. Put your .bib file somewhere with no spaces in the path, like ~/Documents/library.bib, not ~/My Documents/PhD Library/library.bib.

Obsidian Citations plugin

Install the Citations community plugin and point it at your .bib file. Two settings matter here:

Citation database format: BibLaTeX
Literature note folder: wherever you keep reading notes

Then set up a literature note template. This is what every paper’s note looks like when you import it:

---
year: 
author: 
citekey: 
url: 
doi: 
tags:
---

## Abstract


## Notes

The YAML frontmatter gives you filterable metadata across all your literature notes, useful when you’re hunting for everything you read by a particular author or from a particular year. The citekey field is the bridge between your notes and your citations.

To import a paper’s annotations: annotate the PDF in Zotero, right-click and choose Add Note from Annotations, then in Obsidian hit Ctrl+P → Refresh citation database and open the paper’s literature note. Your highlights and comments appear in the Notes section.

Writing the manuscript

To insert a citation, open the command palette and run Insert citation, search by author or title, and it drops [@citekey] into your document. That’s the Pandoc citation syntax; it renders as a properly formatted reference on export.

Install the Pandoc Reference List plugin. It opens a sidebar that renders your bibliography live as you write, formatted in whatever citation style you configure. You can copy it directly into Word if you need to share a chapter draft.

For cross-references, figures, sections, equations, use pandoc-crossref syntax:

# Introduction {#sec:intro}

![Caption here](figures/diagram.png){#fig:diagram}

As shown in @fig:diagram, and further discussed in @sec:intro...

Numbers update automatically on export. You never manually renumber a figure again.

Gotcha: Before exporting, run the Obsidian Link Converter plugin to convert all [[wikilinks]] to standard Markdown links. Pandoc doesn’t understand wikilinks natively, and you’ll get broken references if you skip this.

Exporting

The simpler approach is to embed your bibliography and citation style directly in the document’s YAML frontmatter, so the export command stays short:

---
title: "Thesis Title"
author: Your Name
date: 2026
bibliography: /path/to/library.bib
csl: /path/to/citation-style.csl
fontsize: 12pt
abstract: "Your abstract here."
---

With that in place, the export is just:

pandoc input.md --filter pandoc-crossref --citeproc -o output.pdf

For the full thesis with explicit flags:

pandoc input.md \
  --resource-path /path/to/vault \
  --bibliography /path/to/library.bib \
  --pdf-engine pdflatex \
  --filter pandoc-crossref \
  --citeproc \
  --csl /path/to/citation-style.csl \
  -o output.pdf

The order of --filter pandoc-crossref and --citeproc is not optional: crossref must run before citeproc. Reverse them and your cross-reference labels get mangled.

CSL files for any citation style (APA, Chicago, Vancouver, journal-specific) are available from the Zotero citation styles repository. Download the .csl file and drop it somewhere stable on your machine.

For polished PDF output, use the eisvogel LaTeX template: download eisvogel.tex, place it in ~/.local/share/pandoc/templates/, and add to your export command:

--template eisvogel \
--metadata title="Thesis Title" \
--metadata author="Your Name"

It handles margins, fonts, and chapter headings without any configuration.

If you’re submitting to a journal or working via Overleaf, export to LaTeX instead:

pandoc input.md \
  --natbib \
  --extract-media ./figures \
  -o thesis.tex

--natbib produces proper \cite{} commands; --extract-media copies images out of your vault into a separate folder.

Gotcha: Test the full export pipeline on a small sample file before you run it on your 80,000-word thesis. One broken image path or malformed cite key will abort the whole thing. A three-paragraph test document that exercises citations, a figure, and a cross-reference takes two minutes and saves hours.