Personally, I would do a few more rides and see if the soreness stays or goes away. Your body can adapt to various bike geometries to a point but it won't happen in one ride. Even if you've done a proper bike fit, the geometries between the two bikes are not identical. I was on mountain bikes for 20 years (usually just one bike for a few years at a time), then for various reasons switched to a road bike about a year ago and took a break from mtb. I got back on my existing mountain bike a couple of weeks ago and got sore knees after the first ride. It still took me by surprise because prior to the break I'd ridden this bike for about 4 years with no issues. But that also tells me it's just a matter of body readjusting to the geometry again. I think it's the minor differences in reach and seat tube angle that have an impact on how your knees feel after the first couple of rides. And the cleat position on the shoes if you use clipless pedals.
As a side note, I once switched from concave to convex flat pedals. The convex shape caused me quite a bit of pain in the feet for the first few rides, bad enough that I nearly switched back to the old pedals. But I tried it for a few more rides, the body adapted, and the pain went away.
If your knee pain doesn't go away after the first few rides and you use clipless pedals, I'd start by playing with the position of the cleats on your shoes, and forward/aft position of the saddle on the seat post.