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Existing work demonstrates that animals alternate between engaged and disengaged states during perceptual decision-making. To understand the neural signature of these states, we performed cortex-wide measurements of neural activity in mice making auditory decisions. The trial-averaged magnitude of neural activity was similar in the two states. However, the trial-to-trial variance in neural activity was higher during disengagement. To understand this increased variance, we trained separate linear encoding models on neural data from each state. The models demonstrated that although task variables and task-aligned movements impacted neural activity similarly during the two states, movements that are independent of task events explained more variance during disengagement. Behavioral analyses uncovered that during disengagement, movements become uncoupled to task events. Taken together, these results argue that the neural signature of disengagement, though obscured in trial-averaged neural activity, is evident in trial-to-trial variability driven by changing patterns of spontaneous movements.