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You can pass additional arguments to pandoc through _config.yml. The default configuration is:

pandoc:
  filters:
  extra:
  template:
  meta:
  mathEngine:

• filters is a list of any pandoc filter installed on your path.
• extra is a list of mappings:

extra:
  - key: value

passed to pandoc as --key value.

• template is a template file you wish to use when pandoc generates your posts:

template: dir/.../template.html

will be passed to pandoc as --template=dir/../template.html

The path of the template should be relative to the root of your blog.

For example, the very simple template

$if(toc)$
<div id="$idprefix$TOC">
$toc$
</div>
$endif$
$body$

prepends table of contents to all your posts if variable --toc is also passed. To enable TOC, add to your _config.yml:

pandoc:
  # other options
  extra:
    - toc: # will be passed as `--toc`. Note the colon
  template: dir/../template.html

• meta is a list of anything you wish to be sent to pandoc as meta:

meta:
  - key: value1
  - value2

would be passed as -M key=value1 -M value2.

pandoc-citeproc for example can be configured as:

pandoc:
  filters:
    - pandoc-citeproc
  extra:
    - bibliography: "/path/to/bibfile.bib"
  meta:
    - suppress-bibliography

• mathEngine is an option for choosing math engine. By default, mathEngine is mathjax.

For example, if you want to use KaTeX, you can pass katex to the mathEngine option:

pandoc:
  mathEngine: katex

Then, the args of pandoc is this: [..., "--katex", ...] .