The ability to synchronize body movements with quasi-regular auditory stimuli represents a fundamental trait in humans at the core of speech and music. Despite the long trajectory of the study of such ability, little attention has been paid to how acoustic features of the stimuli and individual differences can modulate auditory-motor synchrony. Here, by exploring auditory-motor synchronization abilities across different effectors and types of stimuli, we revealed that this capability is more restricted than previously assumed. While the general population can synchronize to sequences composed of the repetitions of the same acoustic unit, the synchrony in a subgroup of participants is impaired when the unit’s identity varies across the sequence. In addition, synchronization in this group can be temporarily restored by being primed by a facilitator stimulus. Auditory-motor integration is stable across effectors, supporting the hypothesis of a central clock mechanism subserving the different articulators but critically shaped by the acoustic features of the stimulus and individual abilities.