We studied the effects of fatigue of ankle dorsiflexors on multi-muscle synergies defined as co-varied adjustments of elemental variables (M-modes) that stabilize a task related performance variable (trajectory of the center of pressure, COP). M-modes were defined as muscle groups with parallel changes in activation levels. Healthy participants performed voluntary body sway in the anterior-posterior direction while trying to minimize sway in the medio-lateral direction at 0.25, 0.5 and 0.75 Hz. The trials were repeated before and during fatigue induced with a timed voluntary contraction against a constant load. Factor extraction using the principal component method was used to identify four M-modes within the space of integrated indices of muscle activity. Variance in the M-mode space at different phases across sway cycles was partitioned into two components, one that did not affect the average value of COP shift and the other that did. There were no significant effects of fatigue on variability of performance of the explicit task and on the amplitude of the COP shift. Variance of muscle activation indices and M-mode magnitudes increased during fatigue for muscles (and M-modes) both involved and not involved in the fatiguing exercise. Most of the M-mode variance increase was within the sub-space compatible with the unchanged COP trajectory resulting in an increase of the index of the multi-M-mode synergy. We conclude that one of the adaptive mechanisms to fatigue within a redundant multi-muscle system involves an increase in the variance of activation of non-fatigued muscles with a simultaneous increase in co-variation among muscle activations. The findings can be interpreted within the referent configuration hypothesis on the control of whole-body actions.