Inhibitory control is affected by perceptual processes, but the mechanisms how perceptual features affect response inhibition are poorly understood. Theoretical frameworks detailing how variations in stimulus features that create overlaps between response categories can affect action control, like the Theory of Event Coding (TEC), have not been transferred to inhibitory control. We present a novel Go/Nogo paradigm in which we varied stimulus feature overlap between Go and Nogo trials. To examine what cognitive-neurophysiological subprocesses and functional neuroanatomical structures are modulated by stimulus-response feature overlap and recoding during inhibitory control, we combine event-related potential (ERP) recordings with source localization analyses. We show that response inhibition was compromised when stimulus features overlapped between Go and Nogo trials. The EEG data show that the recoding of stimulus-response mappings induced by such a stimulus feature overlaps affects subprocesses from perceptual gating/categorization (P1 ERP-component) to pre-motor inhibition (Nogo-N2 ERP-component) and motor inhibition (Nogo-P3 ERP-component). Although these are distinct processes, overlapping neuronal structures are associated with these modulations. The cascade of processes starts in the superior frontal cortex and is associated with perceptual categorization mechanisms. Subsequently, pre-motor inhibition or stimulus-response unbinding processes are modulated in parahippocampal structures before stimulus-response rebinding and motor inhibition is accomplished in parahippocampal and superior frontal structures. The study shows how perceptual processes can affect response inhibition using a theoretical framework, which has, until now, not been brought into connection with inhibitory control and establishes links between neurophysiology and functional neuroanatomy of inhibitory control with the TEC framework.