The ability to make decisions based on external information, prior knowledge and context is a crucial aspect of cognition and it may determine the success and survival of an organism. Despite extensive and detailed work done on the decision making mechanisms, the understanding of the effects of arousal remain limited. Here we characterise behavioural and neural dynamics of decision making in awake and low alertness periods to characterise the compensatory signatures of the cognitive system when arousal decreases. We used an auditory tone-localisation task in human participants under conditions of fully awake and low arousal. Behavioural dynamics analyses using psychophysics, signal detection theory and drift-diffusion modelling showed slower responses, decreased performance and a lower rate of evidence accumulation due to alertness fluctuations. To understand the modulation in neural dynamics we used multivariate pattern analysis (decoding), identifying a shift in the temporal and spatial signatures involved. Finally, we connected the computational parameters identified in the drift diffusion modelling with neural signatures, capturing the effective lag exerted by alertness in the neurocognitive system underlying decision making. These results define the reconfiguration of the brain networks, regions and dynamics needed for the implementation of perceptual decision making, revealing mechanisms of resilience of cognition when challenged by decreases in arousal.