Conflict processing has been extensively studied in the context of instructed choices, requiring stimulus-response mapping, but the generalizability of the previously found EEG markers to other contexts of conflict remains elusive. The aim of the present study was to determine if the resolution of a conflict based on action costs requires similar modulations of brain activity than in a classic stimulus-based conflict. 31 participants (15 females) performed an action selection task by reaching with their right arm toward one of two visual targets. In instructed choice trials, participants had to reach the target indicated by a central arrow, surrounded by peripheral arrows which directions could be congruent or not, thus manipulating the level of conflict (flanker task). In free choice trials, the presented stimulus was non-directional and participants could reach the target they preferred. Target positions were manipulated so that one target was biomechanically preferable or both targets were similarly preferable, thus inducing low and high conflict respectively. Results showed that in spite of similar sensory input and motor output, theta power was differently modulated by the context of choice. In instructed choices, midfrontal theta power was significantly enhanced by conflict and correlated with reaction times. In free choices, theta power of a contralateral premotor cluster was modulated according to target choice. Overall, these results suggest that midfrontal theta power constitutes a specific marker of stimulus-based conflict, whereas action-based decisions appear to be better predicted by fluctuations of contralateral premotor theta power.