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Understanding the neural basis of conscious experience and its regulation are fundamental goals of science. While recent research has made substantial progress in identifying the neural correlates of conscious experiences, it remains unclear how individuals exert control over the contents of awareness. In particular, can a memory that has entered the aware state be purged from consciousness if it is not currently desired? Here we tracked the correlates of consciousness in humans using functional magnetic resonance imaging and demonstrated the involvement of a downregulation mechanism that purges contents from conscious awareness. When individuals tried to prevent the retrieval of a memory in response to reminders, hippocampal activity was reduced, as previously established. Crucially, using trial-by-trial reports of phenomenal awareness, we found that this reduction of hippocampal activation was specifically associated with moments when a memory involuntarily intruded into conscious awareness and needed to be purged. This downregulation of activity during memory intrusions appears to disrupt momentary awareness of unwanted contents and, importantly, predicts impaired recall of the memory on later tests. These results tie the voluntary control of phenomenal awareness to observable changes in neural activity linked to awareness, and so provide a neurobiological model for guiding inquiry into the physical foundations of control over consciousness.