Numerous previous studies have shown that masked stimuli trigger cognitive control processes, including the activation of task sets, and thereby affect subsequent processing. However, it has not been directly tested whether unconsciously activated task sets also need to be reconfigured when switching to a new task, as has been shown for consciously triggered task sets. To test whether unconsciously activated task sets are subject to inhibitory processes, we measured n-2 repetition costs following masked cue presentation in a task switching design. We furthermore simultaneously assessed event-related potentials (ERPs) to gain additional insights into task set reconfiguration processes. Results showed that task sets were inhibited following the presentation of an unmasked task cue, as reflected by n-2 repetition costs. Furthermore, a cue-locked positivity ERP component indicated that task sets were reconfigured following both mere task preparation and task execution. In contrast, no evidence for a reconfiguration of unconsciously activated task sets was observed following masked cue presentation in either measure. Thus, task set reconfiguration, including the inhibition of a task set, is likely tied to conscious task set activation, suggesting that an unconscious process - once initiated - is not terminated by inhibitory processes.