The presupplementary motor area (pre-SMA) is considered key in contributing to voluntary action selection during response conflict. Here we test whether individual differences in the ability to select appropriate actions in the face of strong (conscious) and weak (virtually unconscious) distracting alternatives are related to individual variability in pre-SMA anatomy. To this end, we scanned 58 participants, who performed a masked priming task in which conflicting response tendencies were elicited either consciously (through primes that were weakly masked) or virtually unconsciously (strongly masked primes), with structural magnetic resonance imaging. Voxel-based morphometry revealed that individual differences in pre-SMA gray-matter density are related to subjects' ability to voluntary select the correct action in the face of conflict, irrespective of the awareness level of conflict-inducing stimuli. These results link structural anatomy to individual differences in cognitive control ability, and provide support for the role of the pre-SMA in the selection of appropriate actions in situations of response conflict. Furthermore, these results suggest that flexible and voluntary behavior requires efficiently dealing with competing response tendencies, even those that are activated automatically and unconsciously.