In synaesthetes, stimulation of one sensory pathway provokes a sensory experience (e.g. a colour concurrent) in a different sensory modality or sub-modality. Results of synaesthetic Stroop and priming tests indicate that the perception of a colour concurrent interferes with the processing of a veridical colour in synaesthetes. We here examined the congruency between a stimulus’ colour and the colour concurrent both in grapheme–colour synaesthetes and in non-synaesthetes trained on grapheme–colour associations. Electrophysiological (electroencephalogram) and behavioural measurements were collected during a priming task that included grapheme–grapheme and grapheme–colour patch pairs. To investigate covert bidirectional synaesthesia, an additional inverted colour patch–grapheme condition was included. Both groups of participants showed longer reaction time and more negative-going N300 and N400 event-related potential (ERP) components on incongruent trials. Whereas ERP effects in the non-synaesthetes were largely confined to the late cognitive components N300, P300 and N400, the synaesthetes also showed congruency-dependent modulation of the early sensory component N170. Our results suggest that early cognitive processes distinguish cross-modal synaesthetic perceptions from acquired associations. The involvement of both early- and late-stage cognitive components in bidirectional synaesthesia possibly indicates similar feature-binding mechanisms during processing of opposite flow directions of information, namely grapheme–colour and colour–grapheme.