Microalgae offer a sustainable source of omega − 3 fatty acids that can replace fish oil in aquafeeds, but the nutritional benefits are not always clear, particularly when microalgae are used as complete oil replacements in starter feeds. We compared the survival, growth, omega − 3 deposition and composition of the gut microbiota of juvenile mixed‐sex Nile tilapia (Oreochromis niloticus) that had been fed over a 3‐month period on six isonitrogenous, isolipidic and isocaloric aquafeeds that varied only on the contribution of fish oil, soya oil and microalgae (Schizochytrium) oil as lipid sources. Survival was not affected by diet, but fish fed a diet where the entire oil component (5%) was replaced by microalgae oil grew twice as fast as fish fed plant oil or a mixture of plant and fish oil. Dietary omega − 3 content was strongly correlated with omega − 3 deposition in the fish fillet. Complete replacement of fish oil by plant oil caused a significant decrease in the abundance of Peptostreptococcaceae and an increase in the abundance of Aeromonadaceae which is often associated with an inflammatory response in the fish gut. In contrast, when fish and soya oil in the reference diet were replaced by 100% microalgae oil, an increase in Mycobacteriaceae was observed. Our study indicates that Schizochytrium oil can be used to improve the growth of Nile tilapia and increase its omega − 3 content without any of the detrimental effects on the gut microbiome typically associated with some plant oil replacements.