Although a bit dated at this point Geoff Brown had a good course/intro
https://legacy.cs.indiana.edu/~geobrown/book.pdf
In college we did a "Learning how to Learn" type course, and I've used books and reference manuals to learn MCU over the last few decades. I tend to use a "Triangulation" method, where I get multiple topic perspectives, from multiple authors, and forms, and use this to evolve my understanding. It is often a matter to finding the right person to explain something the right way, that leverages knowledge you already have.
For the Cortex-M parts Joseph Yiu has a series of "Essential" books covering the cores with a more user centric perspective than the TRM (Technical Reference Manuals). ST has it's Programming Manuals which are akin to ARM's TRM
There are several college level texts on ARM and RISC processors that might provide context.
Vendors like ST, NXP, ATMEL, etc bolt on their own peripherals to the cores. These are covered in the Reference Manuals, but the concepts can perhaps be gleaned from ancient texts from the like of Zaks or Leventhal, it's just easier these days to put multiple instantiations on the IC / SoC than it was with externally wired peripheral chips.
In more recent years Muhammad Ali Mazidi seems to have taken up a lot of the MCU text book space, perhaps check with Amazon, or other e-book vendors, to see if you find his style amenable.
