Seafood is a key source of long-chain omega-3 fatty acids (FAs) that are important for human health and development. Ocean warming affects the biochemical composition of marine organisms and may reduce levels of omega-3 FAs for some seafood species. However, it is unclear whether this pattern is consistent across species, geography or traits. We investigated the effect of temperature on the amount of key nutritional FAs in marine organisms using a global meta-analysis of 308 experiments across 198 taxa. Each experiment quantified FA levels of a given taxon in at least two controlled environments of different temperatures. We detected an overall trend of lower omega-3 FA levels in the warmer treatments, whilst saturated FA levels were higher. The strong effect in marine algae is particularly concerning because as climate warming continues, a reduction in omega-3 FAs at the base of the food chain may amplify up into primary and secondary consumers and potentially have a large negative impact on human health. Our results will help predict the availability of omega-3 FAs across marine environments to assist with guiding sustainable fishing policies that ensure the security of omega-3 FAs for human societies worldwide