Abstract The prior probability of an upcoming stimulus has been shown to influence the formation of perceptual decisions. Computationally these effects have typically been attributed to changes in the starting point (i.e. baseline) of evidence accumulation in sequential sampling models. More recently, it has also been proposed that prior probability might additionally lead to changes in the rate of evidence accumulation. Here, we introduce a neurally-informed behavioural modelling approach to understand whether prior probability influences the starting point, the rate of evidence accumulation or both. To this end, we employ a well-established visual object categorization task for which two neural components underpinning participants’ choices have been characterised using single-trial analysis of the electroencephalogram. These components are reliable measures of trial-by-trial variability in the quality of the relevant decision evidence, which we use to constrain the estimation of a hierarchical drift diffusion model of perceptual choice. We find that, unlike previous computational accounts, constraining the model with the endogenous variability in the relevant decision evidence, results in prior probability effects being explained primarily by changes in the rate of evidence accumulation rather than changes in the starting point or a combination of both. Ultimately, our neurally-informed modelling approach helps disambiguate the mechanistic effect of prior probability on perceptual decision formation, suggesting that prior probability biases primarily the interpretation of sensory evidence towards the most likely stimulus.