Purpose of the Template

The Obsidian–Zotero integration template allows you to:

• Export annotations, highlights, and attached images from Zotero into Markdown files in your Obsidian vault.

• Uses the Zotero comments as sections.

• Generate Pandoc/PDF-ready figure blocks for images from Zotero PDFs.

• Maintain consistent folder structure and absolute or relative paths for files, making the repository portable.

• Keep citekeys, figure labels, and captions automatically.

Folder Structure in Obsidian

My Obsidian vault setup for this workflow:

MyRepo/                                  # obsidian volt
├── _templates/
│   └── zotero_annotation_template.md
├── zotero_exports/                      # zotero-exported attachments
│   ├── exported_file/
│   │   └── images/
│   │       ├── img1.png
│   │       └── img2.png
│   └── file.md

Explanation

zotero_exports/ → stores PDFs and images exported from Zotero.

exported_file → contains Obsidian Markdown notes generated from Zotero annotations.

templates/zotero_annotation_template.md → your Jinja-style template file.

Usage

1. Place the template.md in your obsidian /_templates folder.

2. Configure your Obsidian–Zotero plugin.

3. Add a new Format:

- Name: format_name

- Output path: zotero_exports/{{citekey}}/{{citekey}}.md
- Image output path: zotero_exports/{{citekey}}/images/
- Image Base Name: {{citekey}}
- Template file: _templates/zotero_annotation_template.md
- Bibliography style: IEEE (use whatever you want, don't forget to change the .csl file)

5. Use the Zotero Integration Plugin (ctrl+p), in Obsidian, and select the file you'd like to export, type the format_name you entered.

Note: I used the preconfigured Zotero template.tex for the example.pdf