Fish oil is primarily extracted from small marine pelagic fishes, reducing their availability for marine wildlife forage and artisanal fishing catches that support food security in lower income coastal nations. A primary use of fish oil is in feeds for aquaculture, the world’s fastest growing food sector. Efforts to transition fed aquaculture to sustainability includes replacing fish oil in aquafeeds with more environmentally responsible alternative ingredients. The heterotrophic marine microalga Schizochytrium sp., one of the first commercialized alternatives, lacks an open-access, systematic analysis of environmental impacts of substituting fish oil with heterotrophic microalgae from biorefineries. This study compared the “cradle to factory-gate” life cycle impacts of fish oil to whole-cell or extracted oil of Schizochytrium combined with canola oil. We conducted an attributional life cycle assessment using inventory data collected from published literature and patents and received feedback on commercial relevance of model assumptions from industry advisors. We examined sugar from a Brazilian sugarcane biorefinery and sucrose from U.S. sugar beets as feedstocks for heterotrophic cultivation of Schizochytrium; and compared life cycle impacts of extracting Schizochytrium oil using solvent-free microwave extraction to conventional solvent extraction. Results were that: cultivation processes had the largest overall effect for both products in both regions; whole-cell Schizochytrium combined with canola oil had significantly lower environmental impacts, in all assessed categories, than Schizochytrium oil blended with canola oil; and conventional solvent extraction had significantly lower environmental impacts compared to solvent-free microwave extraction except global warming potential. Schizochytrium products, compared to fish oil, had substantially lower biotic resource depletion and, in the case of whole cells combined with canola oil, had significantly lower global warming potential but higher impacts for all other categories, primarily because commercial Schizochytrium production used sugar feedstocks as carbon and energy sources. The mix of lower and higher environmental impacts of Schizochytrium products illustrates the importance of openly identifying environmental trade-offs to inform evidence-based decisions for commercial practices. Environmental impacts should also be weighed against potential human health benefits of maintaining omega-3 fatty acids and avoiding contaminants in fish flesh when considering alternatives to fish oil.