While farming is often considered an inherently human activity, many animals also exhibit complex farming behaviours. One of the best-known examples occurs on coral reefs, where territorial damselfish actively maintain and protect an area of turf algae, increasing its dietary quality. In the Caribbean, swarms of mysid shrimp also associate with these damselfish territories, however, the exact nature of this second relationship remains unknown. Here, we show that mysid swarms receive a clear protective benefit from this association, experiencing significantly reduced rates of predation when damselfish are present. However, associating with mysid swarms comes at a cost to damselfish, increasing the time spent defending territory and reducing feeding rates. Despite this, mysid-associated fish are in significantly better condition than fish without associated swarms. This appears to reflect the higher quality turf found within mysid-associated territories, likely due to the high levels of additional nutrients that mysid swarms contribute to the immediate area. In this way, by protecting mysids within their territory, damselfish receive a consistent source of ‘fertilizer’ for their crops. This study represents the first evidence of integrated multi-trophic farming in a fish.