Shoes affect the evolved biomechanics of the foot, potentially affecting running kinematics and kinetics that can in turn influence injury and performance. An important feature of conventional running shoes is heel height, whose effects on foot and ankle biomechanics remain understudied. Here, we investigate the effects of 6–26 mm increases in heel height on ankle dynamics in 8 rearfoot strike runners who ran barefoot and in minimal shoes with added heels. We predicted higher heels would lead to greater frontal plane ankle torques due to the increased vertical moment arm of the mediolateral ground reaction force. Surprisingly, the torque increased in minimal shoes with no heel elevation, but then decreased with further increases in heel height due to changes in foot posture. We also found that increasing heel height caused a large increase in the ankle plantarflexion velocity at heel strike, which we explain using a passive collision model. Our results highlight how running in minimal shoes may be significantly different from barefoot running due to complex interactions between proprioception and biomechanics that also permit runners to compensate for modifications to shoe design, more in the frontal than sagittal planes.