A common flow across most Jekyll projects is to have content files at the root as .md using almost all markdown. and then layouts and includes files (macros) as .html - which only have html in them.
Then the layouts are referenced in metadata of contents pages to give them style.
and the includes files are referenced in a layout (such as a google analytics snippet in head) or in a content page (such as an image gallery) to insert snippets.
So you’ll mix html and markdown in separate files and they get rendered together and you can mix html and markdown in a single .md file as per my first comment
Here is my project aimed at beginners of Jekyll. Made using the quickstart project and plenty of intro docs. I also cover using html inside a .md file there.
I wrote this guide specifically for html in markdown: