Wild fish utilise aquaculture habitats for shelter and/or food resources. It is often assumed that fish respond to feed input, the abundance of the farmed species or the associated assemblage of biofouling which naturally colonises the structural habitats. However, few studies have directly analysed the composition of the diet of fish within aquaculture habitats, and of these most have focused on fed finfish aquaculture. Snapper are commonly present as adults within coastal mussel farms and tend to become a resident species of these farms. Therefore, they are a suitable case study species for exploring differences in diet between natural and aquaculture habitats. This study investigated the gut contents of snapper in soft-sediment habitats within and outside of New Zealand green-lipped mussel farms. Visual gut analysis and DNA metabarcoding methods were used to provide complementary analyses on the composition of gut contents between the mussel farm and natural (i.e., control) sites. Snapper within mussel farms were consistently found to have consumed different prey groups compared to the control snapper. Prey groups identified from mussel farm snapper gut contents could be directly linked to species commonly present in the farms, that is cultured green-lipped mussels, blue mussels and barnacle biofouling. There was good alignment between the visual gut and genetic analyses for the key species identified. Overall, the results show that the highly abundant prey groups consumed by snapper in mussel farm habitats are likely to be beneficial to the snapper population, reducing foraging effort and potentially supplying more nutritious prey. These findings provide evidence towards the supporting services of mussel farm habitats through the provision of food resources.