Hello, I have an existing 12/3 NMB in a jbox in the kitchen. Can I use one circuit for a GFCI Countertop circuit and one circuit for a dedicated microwave circuit that does not need GFI protection and share the neutral? Thank you!

Yes you can.
At the first box you will need to split off to two separate 12/2 cables.
It gets a bit trickier if you want to load out to other receptacles from the GFI.