Stack height is a highly discussed key design feature of running shoes but its effects are not well understood. This study analyzed how shoe stack height and running speed influence full-body running coordination and motor variability structure using an uncontrolled manifold (UCM) analysis. The joint angle variability (i.e. elementary variables) was analyzed in terms of its effects on a synergy stabilizing the center of mass (CoM, i.e. performance variable). A total of 17 healthy experienced runners participated and ran at 10 and 15 km/h on a treadmill with three running shoes differing in stack height (H:​ 50 mm, M:​ 35 mm, L:​ 27 mm). The UCM components (UCM_||, UCM_Ʇ & UCM_ratio) were compared with statistical parametric mapping rmANOVAs for different shoes and speeds. The shoes did not show significant effects for the three UCM components. With increasing speed from 10 to 15 km/h, the joint angle coordination variability affecting the CoM (UCM_Ʇ) increased and UCM_ratio decreased independent of the shoe condition. This indicated that stack height did not influence the motor variability structure. However, independent of the shoes, the variability affecting CoM increased which led to a weakened synergy stabilizing CoM (UCM_ratio). It can be suggested that the variations in the tested running speeds had a greater impact on the running coordination than those of the tested shoes within the UCM framework.