2  yaml for your Quarto book

MathJax is handling the display of your equations in html and you need to set the configuration to show numbers. Oddly, that is not the default. So you need include-in-header: mathjax.html in your Quarto book yaml. See the mathjax tab for your mathjax.html code.

This is what a minimal _quarto.yaml for numbered equations looks like

project:
  type: book

book:
  title: "Quatro for amsmath LaTeX users"
  chapters:
    - index.qmd
    - yaml.qmd
    - numbered_equations.qmd

format:
  html:
    include-in-header: mathjax.html
  pdf:
    include-in-header:
      - text: |
          \usepackage{mathtools}
# Don't use this. Breaks numbering (Aug 2024)
#    html-math-method:
#      method: mathjax
#      url: "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"

August 2024: I don’t know why that url is not working. It was in Jan 2024. It is just setting the MathJax version. Probably the url is out of date somehow.