Pavlovian biases influence learning and decision making by intricately coupling reward seeking with action invigoration and punishment avoidance with action suppression. This bias is not always adaptive-it can often interfere with instrumental requirements. The prefrontal cortex is thought to help resolve such conflict between motivational systems, but the nature of this control process remains unknown. EEG recordings of midfrontal theta band power are sensitive to conflict and predictive of adaptive control over behavior, but it is not clear whether this signal reflects control over conflict between motivational systems. Here we used a task that orthogonalized action requirements and outcome valence while recording concurrent EEG in human participants. By applying a computational model of task performance, we derived parameters reflective of the latent influence of Pavlovian bias and how it was modulated by midfrontal theta power during motivational conflict. Between subjects, those who performed better under Pavlovian conflict exhibited higher midfrontal theta power. Within subjects, trial-to-trial variance in theta power was predictive of ability to overcome the influence of the Pavlovian bias, and this effect was most pronounced in subjects with higher midfrontal theta to conflict. These findings demonstrate that midfrontal theta is not only a sensitive index of prefrontal control, but it can also reflect the application of top-down control over instrumental processes.