Is there an easy way to copy the content of a linux partition into another linux partition

I have a SD card which have a prepped OS partition, that I use for a raspberry pi. Now I made some changes while I was working on a linux machine, and added different files and packages for specific usage, and since I don't want to re-prep the other SD card I was using before, I would like to copy the whole content of a partition from one SD to another.

I cannot copy the partition or SD card as is, since the SD cards have different size, and as such, the partitions have different size too. I was thinking to mount the second SD card and copy all the content from the first SD card (which is what I use to boot the RPI); although I am not sure if that would actually copy all files, including system files. The boot partition is identical, so no need to copy that.
Am I going to hit issues doing so? I also thought to run a VM with debian on my windows machine and copy everything using the VM, but that does not seem to be a better solution than just use the RPI directly.