I was pain free prior to going clipless. Experienced new aches and pains during the first weeks of going clipless.
Both Shimano mtn shoes and Spd pedals. Saddle height played a role as well as cleat placement on the shoe.

The other clipless riders i encountered were most helpful observing and commenting on the " fit, setup " of my pedals. At this point many years later i would never consider not going clipless pedals.