We are generating a PDF using Illustrator which has the correct colors we need. But when we try to generate the same file which contains the exact same image assets programmatically, the colors when printed are off and are not what we need them to be.

Is there a way to modify the color profile of the generated PDF or a way to optimize the colors using Prince so that we can get it to be exactly what we need it to be when printing?

I'm not the best person to answer this, but https://www.princexml.com/doc/color-management/ has some pointers, including how to set the color profile for the generated PDF.

If you still have trouble, are you able to post a simple Illustrator file that shows what you're trying to get, and what HTML file you have so far towards reproducing that PDF from Prince?

Please note that the relevant documentation for the latest Prince release is located here:
https://www.princexml.com/doc/graphics/#color-management

Edited 25 Oct 2021 by csant

Thank you! The documentation helped us solve the issue.