It is well known that performance on a given trial of a cognitive task is affected by the nature of previous trials. For example, conflict effects on interference tasks, such as the Stroop task, are reduced subsequent to high-conflict trials relative to low-conflict trials. This interaction effect between previous and current trial types is called "conflict adaptation" and thought to be due to processing adjustments in cognitive control. The current study aimed to identify the neural substrates of cognitive control during conflict adaptation by isolating neural correlates of reduced conflict from those of increased cognitive control. We expected cognitive control to be implemented by prefrontal cortex through context-specific modulation of posterior regions involved in sensory and motor aspects of task performance. We collected event-related fMRI data on a color-word naming Stroop task and found distinct fronto-parietal networks of current trial conflict detection and conflict adaptation through cognitive control. Conflict adaptation was associated with increased activity in left middle frontal gyrus (GFm) and superior frontal gyrus (GFs), consistent with increased cognitive control, and with decreased activity in bilateral prefrontal and parietal cortices, consistent with reduced response conflict. Psychophysiological interaction analysis (PPI) revealed that cognitive control activation in GFs and GFm was accompanied by increased functional integration with bilateral inferior frontal, right temporal and parietal areas, and the anterior cerebellum. These data suggest that cognitive control is implemented by medial and lateral prefrontal cortices that bias processes in regions that have been implicated in high-level perceptual and motor processes.