Nutrient acquisition through heterotrophy is critical for the health of reef-building corals. The optimization of exogenous nutrition protocols to support a diversity of aquaculture corals requires improved techniques to assess feeding rates. Here, we compared the feeding rates of three coral species (Acropora millepora, Pocillopora acuta and Galaxea fascicularis) fed Artemia salina through capture rate (indirect) and dissection (direct) approaches, with direct detection and enumeration within dissected polyps facilitated by fluorescent microbeads ingested by the Artemia. When A. millepora was provided Artemia at 3 individuals ml−1 for one hour, the calculated capture rates (0.7 ind. polyp−1 h−1) overestimated prey ingested compared to prey detected directly within polyps (0.2 ind. polyp−1 h−1), and ingestion varied significantly between genotypes. In contrast, for P. acuta, capture rate calculations (1 ind. polyp−1 h−1) underestimated prey detected within polyps (3.5 ind. polyp−1 h−1) and ingestion did not vary between genotypes. For G. fascicularis, the feeding rates were similar as calculated by both capture rates (59 ind. polyp−1 h−1) and by polyp dissections (75 ind. polyp−1 h−1). Results from this study provide valuable insights into coral feeding rates of different coral species that can improve prey enrichment and feeding strategies for nutritional supplementation of corals in captivity.