Abstract Previous behavioural and neuroimaging studies have consistently reported that our memory is enhanced for associations congruent or incongruent with the structure of our prior knowledge, termed as schemas. However, it remains unclear if similar effects exist if encoded associations are emotional. Do emotional schemas also facilitate learning and subsequent retrieval? Does it depend on the type of experienced emotions? Using a novel face-word pair association paradigm combined with fMRI and eye-tracking techniques, we demonstrated and replicated in two independent studies that congruency with emotion schemas and emotion category interact to affect associative memory. Overall, emotion schemas facilitated memory for associative context, paralleled by the recruitment of left inferior frontal gyrus (IFG) during successful encoding of emotionally congruent vs. incongruent pairs. However, emotion schema effects differed across two negative emotion categories: disgust and fear, with disgust remembered better than fear. The IFG engagement was higher during successful encoding of congruent vs. incongruent pairs, but only in the case of disgust, suggestive of more semantic processing involved in learning disgust-related associations. On the contrary, the encoding of congruent vs. incongruent fear-related pairs was supported by activity in right fusiform gyrus (FG), suggesting greater sensory processing of faces. Successful memory formation for congruent disgust-related pairs was associated with a higher loading of pupil dilation component related to sympathetic activation, longer gaze time on words compared to faces, and more gaze switches between the two. This was reversed for fear-related pairs where the faces attracted more attention, as reflected by longer gaze time (compared to words). Overall, our results at the behavioural, physiological, and neural level converge to suggest that emotional congruency influences memory similar to semantic schemas. However, encoding processes and neural effects vary depending on emotion category, reflecting the differential role of semantic processing and visual attention processes in the modulation of memory by disgust and fear.