Previous behavioural and neuroimaging studies have consistently reported that memory is enhanced for associations congruent or incongruent with the structure of prior knowledge, termed as schemas. However, it remains unclear if similar effects arise with emotion-related associations, and whether they depend on the type of emotions. Here, we addressed this question using a novel face-word pair association paradigm combined with fMRI and eye-tracking techniques. In two independent studies, we demonstrated and replicated that both congruency with emotion schemas and emotion category interact to affect associative memory. Overall, memory retrieval was higher for faces from pairs congruent vs. incongruent with emotion schemas, paralleled by a greater recruitment of left inferior frontal gyrus (IFG) during successful encoding. However, emotion schema effects differed across two negative emotion categories. Disgust was remembered better than fear, and only disgust activated left IFG stronger during encoding of congruent vs. incongruent pairs, suggestive of deeper semantic processing for the associations. On the contrary, encoding of congruent fear vs. disgust-related pairs was accompanied with greater activity in right fusiform gyrus (FG), suggesting a stronger sensory processing of faces. In addition, successful memory formation for congruent disgust pairs was associated with a higher pupil dilation index related to sympathetic activation, longer gaze time on words compared to faces, and more gaze switches between paired words and faces. This was reversed for fear-related congruent pairs where the faces attracted longer gaze time (compared to words). Overall, our results provide converging evidence from behavioural, physiological, and neural measures to suggest that congruency with available emotion schemas influence memory associations in a similar manner to semantic schemas. However, these effects vary across distinct emotion categories, pointing to a differential role of semantic processing and visual attention processes in the modulation of memory by disgust and fear, respectively.