Build a Pandoc citation workflow

Prepare the sample items

In Zotero, select My Library, then select Add Item by Identifier. Add these two DOIs:

Open each item and replace its Citation Key with the value in the table.

In Obsidian, run ZotLit: Open literature note quick switcher. Select each sample item to create its Literature Note.

Confirm that ZotLit creates zotlitTutorialIoannidis2005.md and zotlitTutorialNosek2015.md. Create one ordinary Obsidian note named Reading plan.

Create a folder named ZotLit Pandoc tutorial inside your Documents directory.

Configure both citation sources

Open Settings > ZotLit > Citations. Turn on Pandoc citations and Wikilink citations.

Under Formatting, install the Pandoc engine. This managed engine formats the References Sidebar and powers built-in export.

Select APA Style 7th edition as the Citation and references style. Its author-date output makes locators and author modes easy to compare.

Create the worked note

Create a Markdown note named Citation workflow check. Run:

Select APA Style 7th edition and set Document language to en-US. Select Save so the native workflow uses this note's style too.

Paste this body into the note:

# Citation workflow check

A plain Literature Note link introduces the first source [[zotlitTutorialIoannidis2005]].

The same source appears with its article locator [[zotlitTutorialIoannidis2005#cite:locator=e124]].

[[zotlitTutorialIoannidis2005#cite:mode=author-in-text&locator=e124]] examines why published research findings may be false.

Nosek et al. propose guidelines for open research [[zotlitTutorialNosek2015#cite:mode=suppress-author&locator=1423]].

Both sources support the comparison [[zotlitTutorialIoannidis2005]]; [[zotlitTutorialNosek2015#cite:locator=1423]].

A literal Pandoc citation names the second source again [@zotlitTutorialNosek2015].

The wider reading list remains an ordinary vault link [[Reading plan]].

Keep the semicolon and both Literature Note links on one line. Together they form one Citation Run.

Review the note in Obsidian

Switch to Live Preview, then run:

The References Sidebar shows two entries. Each source appears once, even though the note cites it several times.

Check the rendered note and sidebar:

• The plain link renders as (Ioannidis, 2005).
• The locator link renders as (Ioannidis, 2005, p. e124).
• The author-in-text link renders as Ioannidis (2005, p. e124).
• The suppress-author sentence ends with Nosek et al. propose guidelines for open research (2015, p. 1423).
• The Citation Run renders as (Ioannidis, 2005; Nosek et al., 2015, p. 1423).
• The literal citation renders as (Nosek et al., 2015).
• Reading plan remains an ordinary vault link.

Export with ZotLit

Keep Zotero open.

Run:

Keep Format set to Word document, choose your ZotLit Pandoc tutorial folder, and select Export. Open the resulting .docx file and repeat the checks from the References Sidebar.

Built-in export uses Better BibTeX to fetch current bibliography data from Zotero.

Save the version-matched integration pair

Open Settings > ZotLit > Citations > Formatting. Under Native Pandoc workflow, find Pandoc integration pair and select Save integration files.

Choose your ZotLit Pandoc tutorial folder. ZotLit saves zotlit-cite.lua and zotlit.yaml there. The pair matches your installed ZotLit version; save a fresh pair after each ZotLit update.

Create the native bibliography file

Save references.json in your ZotLit Pandoc tutorial folder. Include both Zotero items used in the worked note.

In Zotero, right-click My Library. Select Export, choose Better CSL JSON, and enable Keep updated. Save the file as references.json.

Better BibTeX updates the file after the source library or collection changes.

The citation keys in references.json must match the keys used in the worked note.

Run native Pandoc

Keep Obsidian open with this vault active and ZotLit loaded. Replace each path in this command with an absolute path, then run it in a terminal:

pandoc "/absolute/path/to/input.md" --defaults "/absolute/path/to/workflow/zotlit.yaml" --bibliography "/absolute/path/to/references.json" --fail-if-warnings --output "/absolute/path/to/output.docx"

Keep --fail-if-warnings. It stops the run when Pandoc cannot find a cited item in references.json.

Compare the Word documents

Open the native .docx beside the built-in export. Both documents should contain the same two formatted bibliography entries.

Compare the repeated-source formatting, locators, author modes, grouped Citation Run, literal citation, and ordinary vault link. The citation content should agree because both routes start from the same note and style.

The bibliography source differs. Built-in export asks Better BibTeX for current data, while native Pandoc reads the auto-updated references.json file.