Biofloc technology (BFT), which is a recirculating aquaculture system, can significantly enhance nutrients and waste recycling. In addition, heterotrophic microorganisms in the BFT system can convert nitrogenous waste and residual bait produced by the metabolism of the culture species into nutrients, thereby reducing feed requirements. BFT systems are divided into three types based on the circulation of nitrogen: chemoautotrophic, heterotrophic and photoautotrophic. Common bioflocs are mainly chemoautotrophic, and control toxic nitrogen through nitrification. Additional sugars were supplemented to increase the C/N ratio to synthesize the nitrogen source into the biomass through assimilation. The bioflocs of these two energy metabolic pathways have been extensively studied. However, algae often play a prominent role in natural biofloc communities that cannot be explained simply by chemoautotrophy and heterotrophy. Algae absorb CO₂ through photosynthesis to produce O₂ and organic matter that can be used by bacteria. Moreover, it can utilize nitrate produced by nitrite-oxidizing bacteria as a nutritional substrate to support their growth. Loach (Misgurnus anguillicaudatus) is an important freshwater species farmed in China. Traditional loach breeding techniques include pond, paddy, and cage farming. However, these farming methods rely on a substantial quantity of water to manage nitrogen-containing waste in the water body, which places great pressure on the environment and hinders the sustainable, eco-friendly development of aquaculture. To understand the breeding effects of nitrification and photoautotrophic bioflocs as compensatory nutrients, loach was grown in two types of bioflocs for 45 days. Growth performance, digestive enzyme activity, community structure of the water column, as well as gut microbiome and nutritional composition of the two types of flocs were compared. Nitrification and photoautotrophic groups significantly reduced the feed conversion rate compared with the clear water group. Meanwhile, the ABFT group exhibited an enhanced absorption of nitrate (40.93%) and phosphate (37.47%), compared with the BFT group. No significant differences was observed in feed conversion and specific growth rates, or mean final weight between the two groups. The mean final weight of both groups was reduced by 10% and no significant difference was observed in the final density of the nitrification group compared to that of the clear-water group. Nitrification and photoautotrophic bioflocs could provide 36.69±1.17% and 40.20±1.05% of crude protein, respectively. Photoautotrophic bioflocs increased crude fat content and promoted the conversion of saturated to unsaturated fatty acids. The higher protein and crude fat contents of the photoautotrophic group promoted the activity of trypsin and lipase in this group of loaches. Microbial community analysis showed that the addition of algae had no significant effect on the alpha diversity index of mature bioflocs at the phylum or genus level. The ingestion of bioflocs by loaches resulted in a significant decrease in the sobs index of the intestinal flora. The dominant intestinal flora in the nitrification group were Proteobacteria, Actinobacteria, and Chloroflexi, and those in the photoautotrophic groups were Proteobacteria and Cyanobacteria. Increased concentrations of Aeromonas were observed in the ABFT group at the genus level. The high abundance of Aeromonas may have disrupted the balance of the intestinal flora of loaches in the ABFT group, leading to a lower survival rate. Additionally, the bacterial flora detected in both the water and gut reflected the influence of bioflocs on the gut health of the loaches. By substituting a portion of the feed with nitrification and photoautotrophic biofloc, it is possible to partly reduce the feed and most of the water treatment costs, which in turn, lowers the feed conversion rate. Therefore, both types of flocs demonstrate practical value in the breeding of specific species such as loaches. This study establishes a theoretical basis for advancing the integration of specialized aquatic products with innovative farming models.