This study aimed to evaluate the influence of microalgae addition on the physical and functionality of bioflocs and the growth and health performance of giant prawn (Macrobrachium rosenbergii). Three biofloc‐based giant prawn culture systems were compared that is biofloc system without microalgae addition as a control, biofloc system with Chlorella sp. addition and biofloc system with Ankistrodesmus sp. addition. Giant prawn juveniles (2.00 ± 0.10 g) were randomly distributed into 12 units of outdoor fibre tanks (500 L in capacity) at a density of 40 juvenile per tank and maintained for 60 days. Molasses was added at an estimated C/N ratio of 6, and each microalga was added once a week at a density of about 105 cell/mL. The addition of microalgae in biofloc systems did not affect the prawn's survival and immune parameters as well as its robustness against hypoxia stress (p > 0.05). Alkalinity in the microalgae‐added biofloc systems was significantly higher (p < 0.05) than that of the control, whereas total ammonia nitrogen (TAN), nitrite, nitrate, total phosphate and dissolved phosphate were not significantly different amongst the treatments. The addition of Chlorella sp. and Ankistrodesmus sp. resulted in 11% and 18% higher size of biofloc particles, respectively, and altered the fatty acid profile of bioflocs, but did not affect the protein content. In conclusion, Chlorella sp. and Ankistrodesmus sp. addition could increase the particle size and alter the fatty acid profile of bioflocs, but did not affect the water quality and the growth performance of giant prawn in biofloc systems.