Throughout the day, humans show natural fluctuations in arousal that impact cognitive function. To study the behavioural dynamics of cognitive control during high and low arousal states, healthy participants performed an auditory conflict task during high-intensity physical exercise (N= 39) or drowsiness (N= 33). In line with the pre-registered hypothesis, conflict and conflict adaptation effects were preserved during both altered arousal states. Overall task performance was markedly poorer during low arousal, but not for high arousal. Modelling behavioural dynamics with drift-diffusion analyses revealed evidence accumulation and non-decision time decelerated, and decisional boundaries became wider during low arousal, whereas high arousal was unexpectedly associated with a decrease in the interference of task-irrelevant information processing. These findings show how arousal differentially modulates cognitive control at both sides of normal alertness, and further validates drowsiness and physical exercise as key experimental models to disentangle the interaction between physiological fluctuations on cognitive dynamics.Statement of RelevanceThe variability in arousal and alertness that we naturally experience in our everyday activities is rarely considered in cognitive neuroscience frameworks. Here, we presented a Simon task where the word “left” or “right” was heard through the participant’s right or left ear while either exercising at high-intensity or falling asleep, in order to map the behavioural dynamics of cognitive control on both sides of the arousal spectrum. We disentangled different elements involved in decision-making with computational modelling analyses. While basic effects of conflict in cognitive control were preserved regardless of the arousal state, high and low arousal seem to differentially impact decision-making processes. These results emphasise that naturally inducing drowsiness and physical exercise can provide a suitable model to test the resilience of decision-making processes when challenged by arousal and show the resilience of cognitive control mechanisms in face of physiological fluctuations.