Generate a LaTeX-based PDF from Markdown

Generating a PDF from Markdown requires Pandoc and a LaTeX engine. This guide covers the full process: converting Obsidian or Markdown notes into a clickable, navigable PDF with table of contents, headings, and custom headers/footers.

Unlike a simple “Export to PDF” in Obsidian, this method ensures:

• Clickable table of contents
• PDF bookmarks for headings
• Unicode support
• Custom footers and headers
• Full control over layout and fonts

You can run this pipeline locally on Windows, macOS, or Linux. It works with:

1. Markdown files exported from Obsidian
2. Any standard Markdown source
3. Optional LaTeX customization

Prerequisites

• Pandoc  installed and accessible from the terminal
• LaTeX distribution installed, used MikTeX  for Windows here

Check installations

pandoc --version
pdflatex --version

Configure Your LaTeX Header (Optional)

For headers, footers, fonts, and page numbering, create a LaTeX header file, e.g., header.tex:

    \usepackage{fancyhdr}
    \pagestyle{fancy}
 
    \fancyhf{}
    \fancyfoot[C]{\thepage}
    \fancyhead[L]{My Markdown Notes}
    \fancyhead[R]{Generated PDF}
 
    \renewcommand{\headrulewidth}{0.4pt}
    \renewcommand{\footrulewidth}{0pt}

Generate the PDF

1. Basic PDF generation

pandoc "YourNote.md" -o "YourNote.pdf" --toc --pdf-engine=xelatex

• --toc generates a clickable table of contents
• --pdf-engine=xelatex ensures Unicode support and modern font handling

2. PDF generation with custom LaTeX header

pandoc "YourNote.md" -o "YourNote.pdf" --toc --pdf-engine=xelatex -H header.tex

This applies your custom headers, footers, and layout.

Notes on File Organization

• Multiple Markdown files: you can combine them in order:

pandoc chapter1.md chapter2.md chapter3.md -o fullbook.pdf --toc --pdf-engine=xelatex -H header.tex

• Unicode symbols: XeLaTeX or LuaLaTeX is required; pdflatex cannot handle non-ASCII symbols.

• Font customization: set the main font via Pandoc variable:

pandoc "YourNote.md" -o "YourNote.pdf" --toc --pdf-engine=xelatex -V mainfont="Latin Modern Roman" -H header.tex

Verification

After compilation:

• Open the PDF

• Verify that:

• Table of contents links work

• Headings are clickable

• Custom headers and footers appear

• Unicode symbols render correctly