Cognitive fatigue is a problem for the safety of critical systems (e.g., aircraft) as it can lead to accidents, especially during unexpected events. In order to determine the extent to which it disrupts adaptive capabilities, we evaluated its effect on online and anticipatory control. Despite numerous studies conducted to determine its effects, the exact mechanism(s) affected by fatigue remains to be clarified. In this study, we used distribution and electromyographic analysis to assess whether cognitive fatigue increases the capture of the incorrect automatic response or if it impairs its suppression (online control), and whether the conflict adaptation effect is reduced (anticipatory control). To this end, we evaluated the evolution of the performance over time during the Simon task, a classic conflict task that elicits incorrect automatic responses. To accentuate the presence of fatigue during the Simon task, two groups previously performed a dual-task with two different cognitive load levels to create two different levels of fatigue. The results revealed that time on task impaired online control by disrupting the capacity to suppress the incorrect response but leaving unaffected the expression of the automatic response. Furthermore, participants emphasized speed rather than accuracy with time on task, with in addition more fast guesses, suggesting that they opted for a less effortful response strategy. As the implementation of the suppression mechanism requires cognitive effort, the conjunction of these results suggests that the deficits observed may be due to disengagement of effort over time rather than reflecting an incapacity to make an effort.