Zettlr Setup Guide

​

Overview

• @citekey autocomplete using your Better BibTeX citation keys from Zotero
• LaTeX math formulas rendered in real-time
• Visual table editor for results and comparisons
• Export to Word/PDF/LaTeX for journal submission
• Projects for organizing multi-chapter documents
• Open source with no vendor lock-in

​

When to Use Zettlr vs Obsidian

• Daily research notes
• Literature note-taking from Zotero
• Building connections between ideas
• AI conversation storage
• Synthesis and theory development

• Drafting journal articles
• Writing dissertation chapters
• Papers with heavy citations
• Documents with math formulas/equations
• Exporting to Word/LaTeX/PDF for submission

Zotero          Research Rabbit      Obsidian           Zettlr           Journal
(References) →  (Discovery)      →   (Synthesis)    →   (Drafting)   →   (Submission)
                                     [Web of notes]     [Linear paper]

​

Step 1: Install Zettlr

​

1.1 Download and Install

1. Visit zettlr.com/download
2. Download for your operating system (macOS, Windows, Linux)
3. Install the application
4. Launch Zettlr

​

1.2 First Launch Configuration

1. Choose a workspace folder (can be the same as your Obsidian vault or separate)
2. Select your preferred theme (Light or Dark)
3. Configure editor settings (line numbers, spellcheck language)

​

Step 2: Connect to Zotero (CRITICAL)

​

2.1 Export Better BibTeX Library from Zotero

1. In Zotero: File → Export Library
2. Format: Better CSL JSON (recommended) or Better BibTeX
3. Check: ✅ “Keep updated” (auto-sync when library changes)
4. Save location: Choose a stable location like:
   Copy

   /Users/[username]/Zotero/exports/My-Library.json
   

5. Click OK

​

2.2 Configure Citation Database in Zettlr

1. In Zettlr: Preferences → Export
2. Under “Citation Database”:
   • Click “Add Database”
   • Navigate to your exported library file (e.g., My-Library.json)
   • Click “Open”
3. Verify: You should see the database path listed

​

2.3 Test Citation Autocomplete

1. Create a new file in Zettlr
2. Type @ followed by a few letters from any author’s last name
3. You should see autocomplete suggestions!
4. Select a citation → it inserts as [@smith2024a]

​

2.4 Configure Citation Style

1. Preferences → Export → Citation Style
2. Default is Chicago style
3. To change: Download .csl file from Citation Style Language
4. Common academic styles:
   • APA 7th edition
   • MLA 9th edition
   • Harvard
   • IEEE
   • Nature
   • Your journal’s specific style

​

Step 3: Core Writing Features

​

3.1 Citations with @citekey (The Killer Feature!)

• Parenthetical: [@smith2024a] → (Smith, 2024)
• In-text: @smith2024a → Smith (2024)
• With page: [@smith2024a, p. 45] → (Smith, 2024, p. 45)
• Multiple: [@smith2024a; @jones2024b] → (Smith, 2024; Jones, 2024)

• Type @ and start typing author name
• Fuzzy search works (type @smi finds Smith, Smithers, etc.)
• Arrow keys to select, Enter to insert
• Bibliography auto-generates in preview

As @coviello2024 argues, organizational scaling requires...

However, this view has been contested [@mithani2023; @sanasi2025],
particularly regarding digital business models.

The framework proposed in [@palmie2023, pp. 234-236] suggests...

​

3.2 Math Formulas with LaTeX

The regression model is $y = \beta_0 + \beta_1 x + \epsilon$

$$
\begin{aligned}
E[Y|X] &= \beta_0 + \beta_1 X \\
R^2 &= 1 - \frac{SS_{res}}{SS_{tot}}
\end{aligned}
$$

• Statistical models
• Economic equations
• Mathematical proofs
• Chemical formulas
• Algorithmic notation

​

3.3 Visual Table Editor

1. Click the “Insert Table” button (or Cmd/Ctrl+T)
2. Select grid size (rows × columns)
3. Edit cells directly - Tab to navigate
4. Right-click for options:
   • Add/remove rows
   • Add/remove columns
   • Align columns (left/center/right)

| Model | AIC | BIC | R² |
|-------|-----|-----|-----|
| Model 1 | 245.3 | 267.8 | 0.42 |
| Model 2 | 238.1 | 264.9 | 0.51 |

​

3.4 Comments for Drafting

This section discusses the methodology. <!-- Example: TODO reminder for later revision -->

Our findings suggest that... <!-- Example: Check citation against source -->

• Leave notes to yourself
• Mark sections for revision
• Hide text temporarily without deleting
• Add reviewer responses (invisible in export)

​

Step 4: Projects for Long Documents

​

4.1 Create a Project

1. Create a folder structure:
   Copy

   /My-Dissertation/
   ├── 01-Introduction.md
   ├── 02-Literature-Review.md
   ├── 03-Methodology.md
   ├── 04-Results.md
   ├── 05-Discussion.md
   └── 06-Conclusion.md
   

2. Right-click the folder → Properties
3. Check “Treat as project”
4. Folder turns red with special icon

​

4.2 Configure Project Export

1. Click the folder
2. Configure:
   • Title page information
   • Export formats (PDF, DOCX, etc.)
   • Table of contents settings
   • Bibliography options

​

4.3 Compile Your Paper

1. Right-click project folder → Export Project
2. Zettlr concatenates all files in order
3. Generates single output with:
   • Proper citations
   • Formatted bibliography
   • Table of contents
   • Page numbers

​

Step 5: Export Workflow

​

5.1 Export to PDF (via LaTeX)

• LaTeX distribution installed (MacTeX, MiKTeX, or TeX Live)

1. Cmd/Ctrl+E or click “Share” icon
2. Choose “PDF (LaTeX)”
3. First export may take time (downloading packages)
4. Result: Professional PDF with formatted bibliography

​

5.2 Export to Word (.docx)

1. Cmd/Ctrl+E → “Word (docx)”
2. Opens in Microsoft Word or compatible app
3. Citations formatted according to CSL style
4. Bibliography auto-generated at end

• Journal submissions requiring Word
• Collaboration with non-markdown users
• Track changes and comments in Word

​

5.3 Export to LaTeX Source

1. Export → “LaTeX”
2. Generates .tex file
3. Compile with your own LaTeX editor
4. Full control over LaTeX formatting

​

5.4 Configure Export Settings

• Paper size: A4 or Letter
• Font: Choose academic font (Times, Palatino)
• Line spacing: 1.5 or 2.0 for drafts
• Bibliography style: Select your .csl file
• Remove ZKN IDs: Check this for clean output

​

Step 6: Integration with Research Memex Workflow

​

6.1 From Obsidian to Zettlr

1. In Obsidian: Create synthesis notes with key arguments
2. Copy to Zettlr: Create new .md file for paper section
3. Transform: Convert bullet points → paragraphs
4. Add citations: Use @citekey for every claim
5. Export: Generate PDF/Word when ready

<!-- In Obsidian (synthesis note) -->
## Key Theme: Scaling requires both strategy and structure
- Coviello 2024: Distinguishes scalability from scaling
- Mithani 2023: Digital vs non-digital models differ
- Sanasi 2025: Experimentation structures growth

<!-- In Zettlr (paper draft) -->
The literature reveals that successful scaling requires both
strategic vision and organizational structure [@coviello2024].
This is particularly evident in the distinction between digital
and non-digital business models [@mithani2023], where the role
of experimentation differs significantly [@sanasi2025].

​

6.2 From AI Conversations to Structured Sections

1. Export Cherry Studio conversations to markdown
2. Review AI-generated synthesis
3. Copy useful passages to Zettlr
4. Add proper citations (AI can hallucinate these!)
5. Verify every claim against your Zotero library

​

6.3 Zotero → Zettlr Direct Citations

1. Know your citation key from Zotero (e.g., smith2024a)
2. In Zettlr: Type @smith → autocomplete suggests it
3. Select → inserts [@smith2024a]
4. Export → bibliography auto-generated

​

Step 7: Best Practices

​

7.1 When to Switch from Obsidian to Zettlr

• Exploring new topics
• Taking literature notes
• Building conceptual frameworks
• Connecting ideas across papers

• You have a clear paper outline
• Ready to draft linear sections
• Need citations in final format
• Preparing for submission

​

7.2 File Organization Strategy

/Research-Papers/
├── Drafts/
│   ├── Paper-2025-Scaling/
│   │   ├── 01-Introduction.md
│   │   ├── 02-Literature.md
│   │   ├── 03-Methods.md
│   │   └── ...
│   └── Dissertation/
│       ├── Chapter-1-Introduction/
│       └── Chapter-2-Theory/
├── Submitted/
└── Published/

​

7.3 Version Control with Git

cd /Research-Papers/Paper-2025-Scaling/
git init
git add *.md
git commit -m "Initial draft of introduction"

• Track every revision
• Revert to earlier versions
• Collaborate via GitHub
• Never lose work

​

7.4 Collaborative Writing

• Push to GitHub private repo
• Collaborators pull, edit, push
• Merge changes
• Requires Git knowledge

• Export to .docx
• Share via email/cloud
• Collaborators use Track Changes
• Import revisions back to markdown

​

Step 8: Keyboard Shortcuts for Speed

• Cmd/Ctrl+E: Export document
• Cmd/Ctrl+B: Bold
• Cmd/Ctrl+I: Italic
• Cmd/Ctrl+K: Insert link
• Cmd/Ctrl+Shift+C: Insert comment
• Cmd/Ctrl+T: Insert table
• Cmd/Ctrl+F: Search
• Cmd/Ctrl+R: Replace

• Type @ → Citation autocomplete
• Type # → Headings
• Type $ → Inline math
• Type $$ → Display math

​

Step 9: Advanced Features

​

9.1 Zettelkasten IDs (Optional)

• Format: [[202501151420]] (timestamp-based IDs)
• Auto-generated with Cmd/Ctrl+L
• Creates unique identifiers for notes

​

9.2 Custom CSS for Styling

1. Preferences → Display → Custom CSS
2. Add custom styles for preview
3. Example: Change heading colors, font sizes, etc.

​

9.3 Snippet Manager

1. Preferences → Snippets
2. Add snippets with shortcuts
3. Examples:
   • @@email → your email address
   • @@affiliation → your institution
   • @@template → paper template structure

​

Step 10: Troubleshooting

​

Citation Library Not Loading

• Verify library path in Preferences → Export
• Check file format (must be CSL JSON or BibTeX)
• Re-export from Zotero with “Keep updated”
• Restart Zettlr

​

Export to PDF Fails

• Install LaTeX distribution:
  • macOS: MacTeX (4GB) or BasicTeX (100MB)
  • Windows: MiKTeX
  • Linux: TeX Live
• Or export to Word instead (no LaTeX needed)

​

Bibliography Not Appearing

• Ensure citation style (.csl) is selected
• Check that you have at least one citation in the document
• Try exporting to different format
• Verify Better BibTeX export is up-to-date

​

Math Formulas Not Rendering

• Check syntax: no spaces after $ in inline math
• Verify you’re in preview mode (Cmd/Ctrl+Alt+E)
• Test with simple formula: $x^2$
• Check KaTeX documentation for supported commands

​

Integration with Research Memex Workflow

​

Complete Workflow Example

• Zotero: Collect 50+ papers, configure Better BibTeX
• Research Rabbit: Expand citation network
• Obsidian: Take literature notes, synthesize themes

• Cherry Studio: AI-powered analysis of patterns
• Obsidian: Build conceptual framework
• Zotero: Refine collection, verify citations

• Zettlr: Draft paper sections
  • Use @citekey for every claim
  • Add math formulas where needed
  • Build results tables
• Export: Generate PDF for advisor review

• Zettlr: Incorporate feedback
  • Use comments for tracking changes
  • Update citations
  • Refine arguments
• Export: Final submission to journal

​

Tool Handoff Points

1. Identify completed synthesis notes in Obsidian
2. Create new Zettlr file for paper section
3. Copy key arguments and evidence
4. Transform from notes → prose
5. Add proper citations with @citekey

1. Export Zettlr paper to markdown
2. Save in Obsidian vault for archiving
3. Link to related research notes
4. Track published work

​

Checklist

• Installed Zettlr
• Connected to Zotero Better BibTeX library
• Tested @citekey autocomplete
• Configured citation style (e.g., APA, MLA)
• Created a test document with citations
• Inserted a math formula (if needed)
• Created a table
• Exported to PDF or Word successfully
• (Optional) Created a project for multi-file paper
• (Optional) Installed LaTeX for PDF export

# Test Paper

As @[yourcitekey] demonstrates, the methodology...

The model is: $y = \beta x + \epsilon$

## References
(Auto-generated)

​

Quick Reference

​

Obsidian vs Zettlr Decision Matrix

​

Essential Keyboard Shortcuts

​

Resources

​

Zettlr Documentation

• Citation Guide
• Tables
• Math Formulas
• Projects
• Export Formats
• Writing Markdown in Zettlr
• File Renaming (Zotero)

​

Integration with Other Tools

• Zotero Setup Guide - Configure Better BibTeX citation keys
• Obsidian Setup Guide - Research note-taking
• Cherry Studio Setup Guide - AI-powered analysis

​

External Resources

• Citation Style Language - Download .csl files for any journal
• Pandoc Documentation - Zettlr’s export engine
• KaTeX Documentation - Math formula reference
• Zettlr Forum - Community support

​

Common Questions

​

Next Steps

1. Install Zettlr and connect to your Zotero library
2. Create a test document with 3-5 citations
3. Export to PDF or Word to verify setup
4. Start drafting your next paper section in Zettlr
5. Keep using Obsidian for research notes and synthesis