Move Your Thesis from Word to Plain Text

For researchers outside STEM with chapters already in Word and a university template to follow: bring them into plain text in an afternoon, keep your Zotero citations, and still hand in a Word file

For PhD researchers outside STEM: convert your Word chapters to Quarto, keep your Zotero citations, and get your thesis back as one Word file in your university’s template. Tested, with a downloadable example.
Author

Behzad Samadi

Published

October 3, 2026

این نوشته به فارسی

You already have chapters. They are in Word, they have Zotero citations in them, and your university has given you a template the final thesis must follow. You also have the files: chapter3_final.docx, chapter3_final_v2.docx, chapter3_FINAL_after_supervisor.docx. And the evening when Word renumbered every footnote, or the bibliography broke the night before a deadline.

This article starts where you are. In one afternoon you can move those chapters into plain text, keep every citation, and get your thesis back as one Word file in your university’s template, with a bibliography made for you. From then on you write in plain text, and Word is just what you hand in.

It’s written for researchers in history, philosophy, education, law, the social sciences and literature: people who have never used GitHub and have no wish to become programmers. Everything here was tested on two real Word chapters before it was written, on Windows, Mac and Linux, and the example is yours to try.

What “plain text” means here

Your chapters become files you can open in any program, today or in thirty years. They use a few marks, called Markdown, that look almost like an email:

# The Archive and Its Silences

## Reading against the grain

Colonial records were *not* neutral. As Stoler argues,
the archive is a site of knowledge production [@101, page 47].

A remark for the margin.^[This becomes a footnote.]

# is a chapter heading and ## a section, *word* is italic, [@101, page 47] is a citation from your Zotero library, and ^[...] is a footnote. You don’t format anything while you write: fonts, spacing, numbering and the citation style are applied in one step at the end, from your university’s template.

You won’t type most of these by hand anyway. Your Word chapters are converted for you, and the editor below can show your text the way a word processor does.

What you need

  • Zotero, which you probably use already.
  • Positron, a free editor from Posit, the company behind Quarto, made for researchers. It shows your chapters either as marked-up text or, in visual mode, much like a word processor.
  • pixi, which installs the tools your thesis needs, Quarto and Pandoc, the same versions on Windows and Mac, without an installer or administrator rights. You install it once with one line:
    • Windows (PowerShell): powershell -ExecutionPolicy Bypass -c "irm -useb https://pixi.sh/install.ps1 | iex"
    • Mac (Terminal): curl -fsSL https://pixi.sh/install.sh | sh
  • An AI assistant that can work with files on your computer, such as Claude Code or Codex. It’s optional, but it makes the move painless. More on what it may and may not do below.

Try it first on our example

Before touching your own thesis, try the whole path on ours: the thesis starter. Download it as a ZIP and unzip it, or, if you use GitHub, choose Use this template. It contains two example chapters written in Word, with Zotero citations, a footnote, a table and an image, and an example university template: double-spaced Times New Roman, centred chapter headings, a wide binding margin and a running header.

Unzip it, open the folder in Positron, open the Terminal tab, and paste these three lines one at a time:

pixi install
pixi run import
pixi run word

The first installs Quarto and Pandoc for this folder only. The second converts the Word chapters. It will tell you one thing to do: chapter 2 ends with a pasted bibliography, which you delete, because Quarto makes the bibliography itself. The third makes _book/Archives-and-Their-Silences.docx. Open it. The chapters are in the template’s styles, the citations read “(Stoler 2009, 47)”, and the bibliography is at the end.

Move your own chapters

  1. In Word, accept all tracked changes in each chapter. The import refuses a chapter that still has some, and tells you which.
  2. In the starter folder, delete the two example chapters from word/ and put yours there, named in order: 01-introduction.docx, 02-literature.docx, and so on.
  3. Replace template.docx with your university’s template, under the same name. At Concordia or Stanford, skip this step and see Concordia and Stanford.
  4. In _quarto.yml, put your title and name in place of the example’s.
  5. Run pixi run import, then pixi run word.

Or ask your AI assistant to do it. Open the folder and say something like:

My thesis chapters are in word/ and my university’s template is template.docx. Follow AGENTS.md: import the chapters, show me anything you need me to decide, and make the Word file. Do not change any of my wording.

The folder includes an AGENTS.md that gives the assistant the rules, starting with that last one, and tells it what to check: every heading, footnote, table, image and citation.

What comes across, and what you do by hand

We tested this before writing it. What came across intact:

  • Citations inserted with Zotero (or Mendeley) in Word become real citations, and the details of each source come with them, so the bibliography is rebuilt from your own library data.
  • Headings, italics, footnotes, tables and images.

What you do yourself:

  • Accept tracked changes before importing (step 1).
  • Delete a bibliography you pasted at the end of a chapter. The import tells you where.
  • Citations you typed by hand, not inserted with Zotero, stay as plain text. Your assistant can list them; you link them.
  • Citation keys come out as numbers, like @101. They work. If you’d like readable ones, like @stoler2009, your assistant can rename them.

Your university’s template

The template controls the look of the Word file: fonts, spacing, heading styles, margins, headers and page setup. Change the template and every chapter follows.

It doesn’t bring its content. A title page or declaration printed inside the template won’t appear in the output. Most people add those pages to the final Word file at the end, which takes a few minutes once.

Most universities also want two more things: roman page numbers for the front pages, and a PDF to submit.

  • The PDF comes from pixi run pdf, whatever your university. It fills in the table of contents and saves PDF/A, the archival PDF many universities ask for. It needs LibreOffice (free), installed once.
  • The front pages and their numbering, for a university the starter doesn’t know yet: add the title page and the roman numbers in the final Word file. Word numbers them with a section break before chapter 1.

Concordia and Stanford

For these two universities the starter does all of it: the front pages, their numbering, and the PDF/A.

  • Concordia: pixi run concordia, once, downloads the School of Graduate Studies’ official template and builds its styles on your computer. In _quarto-concordia.yml you fill in your degree (doctoral or master’s), title, committee and abstract. You get the title page and signature page (i and ii, not numbered), the abstract and other front pages from iii, and the chapters from 1.
  • Stanford: there is no official template, so pixi run stanford builds one from Stanford’s published rules. The title page is laid out as Stanford’s specimen pages; the abstract is page iv, because Axess adds the copyright and signature pages itself; the inner margin is 1.5 inches.

Then switch the university on: two lines in _quarto.yml. Check the result against your university’s own rules before you submit; neither university made or checked the starter. More universities will follow; tell us yours (below).

Writing from now on

Open a chapter in Positron. Write as you would anywhere; switch to visual mode if you prefer a page that looks like a document. Insert citations from your Zotero library, and add footnotes and headings from the menus or with the marks above. Run pixi run preview to see the thesis update in your browser as you save, and pixi run word whenever you need the Word file.

“But my supervisor uses Word”

That’s fine. Send them the Word file from pixi run word. They comment and track changes as always. Read their comments and make the changes in your chapter files, which stay the master copy. Every edit passes through your hands, which is what revision should be anyway.

If you write in Persian, Arabic or another right-to-left language

In _quarto.yml, remove the # from two lines, lang: fa (or your language’s code) and dir: rtl. The Word file then runs right to left. We checked: the paragraphs come out marked right-to-left. Set your font in the template’s styles, and every chapter uses it. Leave PDF for later; Word is what you’ll hand in.

Where an AI assistant helps, and where it mustn’t

It can do the clerical work: the import, checking each chapter against its Word original, finding citations typed by hand, renaming citation keys, explaining an error. It must not write your argument. Your university has rules on this, and your examiners are reading for your thinking. The AGENTS.md in the starter says so in its first rule.

Slides from the same text

When the defence comes, Quarto makes slides from the same files: a few headings and points per slide, and your university’s PowerPoint template as the look. That’s a later article.

Later: a history of every change

Once this feels normal, you can keep the folder in a version history with GitHub Desktop, which works with buttons rather than commands: every meaningful step saved with a note, and any earlier version of any paragraph a click away. Optional, and another article.

What it doesn’t do well

  • Very complex tables may need redoing after the import; the assistant will tell you which.
  • The template’s own pages (title page, declaration) are added at the end, as above, unless your university is one the starter already knows.
  • Journals with their own Word template take the same approach: their template becomes template.docx for that article.

Start with our example this week, then your shortest chapter. If you find yourself thinking about your argument instead of your margins, it was worth it.

Where the starter lives: eLearningHub

The thesis starter is part of eLearningHub: coding for the rest of us. It’s where we keep small, ready-to-use projects for people who have never thought of themselves as programmers. You download one, it runs on Windows or Mac, and it does one job well, with instructions an AI assistant can follow.

Besides the thesis starter, there are slide templates in the styles of Stanford and Concordia, for the day of the defence, and an academic project template that turns a paper into a project page. New ones will follow the articles here.

If you try this and get stuck, tell us where, on Collegica’s Facebook page or by replying to the newsletter. The next articles follow the questions you send.