I had the exact same after a ride where I pushed the ball of my foot onto my pedals too hard. This was on a road bike with stiff shoes though. For my MTB rides, I have Specialized Trail Traction shoes, which have stiff soles and are very comfortable.
Since I am running as well, my physio blamed the running though and gave me some foot and toe exercises to strengthen my foot. I was told to stop running up steep hills (which stretches the big toe a lot). Combined with replacing old running shoes more often, putting the cleats as far back as possible on my bike shoes (road and MTB), and focusing on dividing the pressure over the entire width of my foot, it gradually went away (over the course of a year in my case).
I looked into cleat shims a bit to alter the pressure divide, but never actually tried them.
Last edited by BikePiet; 08-07-22 at 09:10 AM.