Corals that support close associations with fish in situ have demonstrated increased growth and thermal tolerance. To test if these benefits could be applied to captive reared corals and identify potential underlying host biochemical and associated microbial responses, we cultured wild-collected Pocillopora verrucosa fragments with various combinations of live feeds and schools of juvenile Chromis viridis damselfish over a 3-month period. While the presence of fish wastes and feeds had a limited effect on Symbiodiniaceae photosynthesis yields, these treatments enhanced coral growth. Total lipid concentrations were similar across field colonies, corals acclimated to captivity, and corals in the experimental treatments, however all captive corals demonstrated a significant reduction in storage lipid concentrations compared to field corals. Fatty acid analysis indicated these shifts were likely the result of higher heterotrophic nutrient acquisition through feeding in field corals. Microbial communities associated with coral tissues were influenced by the presence of different feeds and fish. Despite utilising a mixed fish-coral culture system, significant effects of captivity are observed on coral physiology, which has implications for the health status of corals cultured for replanting degraded reefs or to supply the ornamental trade.