If you are writing a book, presumably you would have each chapter in a separate markdown file.

So, then you convert each chapter file to pdf, and then join the pdfs.

You can inline LaTeX chapter/section break commands even when processing Markdown, and in several ways (dropping \newpage directly in the content before chapters, using header templates, as YAML metadata in the Markdown file, even on the command line).

Google has many examples; one's here using a header file: https://medium.com/@sydasif78/book-creation-with-pandoc-and-...

More are here, including an example using the header-includes YAML metadata param: https://github.com/Wandmalfarbe/pandoc-latex-template/issues...