Abstract The last two decades of electrophysiological and neuroimaging research converged that the activity in the medial frontal cortex plays a pivotal role in cognitive control processes. Notably, the midfrontal theta (MFT) oscillatory EEG power as well as activity in the anterior midcingulate cortex (aMCC) or pre-supplementary motor area (preSMA) were consistently proclaimed as markers of conflict processing. However, these brain signals are strongly correlated with response time (RT) variability in various non-conflict tasks, which overshadows the true nature of their involvement. Our previous study (Beldzik et al., 2022) successfully identified these brain signals during a simultaneous EEG-fMRI experiment implementing Stroop and Simon tasks. Based on the assumption that overcoming the habitual prepotent response during high interference trials requires additional neural resources beyond simple decision variable represented in RTs, here we aim to verify if these markers exhibit a congruency effect beyond RT variations. Furthermore, we explored if these brain signals represent either proactive or reactive cognitive control mechanisms by investigating two widely known behavioral phenomena observed in conflict tasks: proportion congruency and congruency sequence effects. The results revealed partially null findings for MFT activity, yet a distinct cognitive control specialization between aMCC and preSMA. Our study provides novel evidence that the former is involved in proactive control mechanisms, possibly contingency learning, whereas the latter reflects reactive control mechanisms by exhibiting a strong congruency effect regardless of RT variation and responding to adaptive behavior.