Zotero MDNotes Guide

Zotero MDNotes Guide

A skill for exporting Zotero items, annotations, and notes to structured Markdown files for use in knowledge management systems like Obsidian, Logseq, or plain Markdown workflows. Based on zotero-mdnotes (1K stars), this skill creates a bridge between your reference library and your personal knowledge base.

Overview

Zotero is excellent for managing references and reading PDFs, but its note-taking capabilities are limited compared to dedicated knowledge management tools. MDNotes solves this by exporting Zotero data to Markdown files that can be used in any Markdown-compatible system. Each exported file contains bibliographic metadata, your annotations, and your notes in a structured, interlinked format.

This approach gives researchers the best of both worlds: Zotero's powerful reference management with the flexibility and interconnection capabilities of Markdown-based knowledge systems.

Configuration

Template System

• MDNotes uses Nunjucks-based templates to control the output format
• Default templates produce well-structured Markdown with YAML frontmatter
• Templates can be customized to match your preferred note structure
• Separate templates exist for item metadata, annotations, and combined notes
• Template variables provide access to all Zotero metadata fields

Key Configuration Options

• Output directory: where exported Markdown files are saved
• File naming convention: citation key, title, or custom pattern
• Frontmatter fields: which metadata fields to include in YAML header
• Annotation grouping: by color, type, page, or section
• Link format: wiki-links, Markdown links, or plain text references

Frontmatter Configuration

• Title, authors, year, journal, DOI are standard frontmatter fields
• Tags from Zotero are converted to note tags
• Custom fields can be added (read status, rating, project association)
• Zotero item key is included for bidirectional linking
• Date fields use ISO 8601 format for consistent sorting

Export Workflows

Single Item Export

• Right-click a Zotero item and select the MDNotes export option
• Choose between metadata only, annotations only, or combined export
• The plugin generates the Markdown file in the configured output directory
• If a file with the same name exists, choose to overwrite or create a new version