In this study, we leveraged the high temporal resolution of EEG to examine the neural mechanisms underlying the flexible regulation of cognitive control that unfolds over different timescales. We measured behavioral and neural effects of color–word incongruency, as different groups of participants performed three different versions of color–word Stroop tasks in which the relative timing of the color and word features varied from trial to trial. For this purpose, we used a standard Stroop color identification task with equal congruent-to-incongruent proportions (50%/50%), along with two versions of the “Reverse Stroop” word identification tasks, for which we manipulated the incongruency proportion (50%/50% and 80%/20%). Two canonical ERP markers of neural processing of stimulus incongruency, the frontocentral negative polarity incongruency wave (NINC) and the late positive component (LPC), were evoked across the various conditions. Results indicated that color–word incongruency interacted with the relative feature timing, producing greater neural and behavioral effects when the task-irrelevant stimulus preceded the target, but still significant effects when it followed. Additionally, both behavioral and neural incongruency effects were reduced by nearly half in the word identification task (Reverse Stroop 50/50) relative to the color identification task (Stroop 50/50), with these effects essentially fully recovering when incongruent trials appeared only infrequently (Reverse Stroop 80/20). Across the conditions, NINC amplitudes closely paralleled RTs, indicating this component is sensitive to the overall level of stimulus conflict. In contrast, LPC amplitudes were largest with infrequent incongruent trials, suggesting a possible readjustment role when proactive control is reduced. These findings thus unveil distinct control mechanisms that unfold over time in response to conflicting stimulus input under different contexts.