Farfantepenaeus paulensis juveniles (72 ± 24 mg), were reared in a suspended microbial flocs system and fed practical diets containing increasing amounts of crude protein (250, 300, 350, 400 and 450 g kg−1 CP). Development of microbial flocs was promoted by high aeration rates and fertilization with wheat bran and molasses. Flocs were composed of detritus in the form of flocculated matter colonized by heterotrophic bacteria, cocoid and filamentous cyanobacteria, flagellate and ciliate protozoa and rotifers. Proximate composition analysis of the suspended microbial floc showed CP levels of 304 g kg−1. After 45 days, mean shrimp survival were above 89%, with no significant differences between treatments. Shrimp fed diets with 350 g kg−1 or higher CP content achieved significant higher (P < 0.05) final weight (0.66–0.68 g), weight gain (0.58–0.61 g) and instantaneous growth rate (0.049–0.050), with feed conversion rates (2.17–2.30) significantly lower (P < 0.05). Results show that, when rearing is carried out in a suspended microbial flocs system, dietary CP levels can be kept at 350 g kg−1. Furthermore, results confirm that microbial-based systems allow shrimp culture without compromising the surrounding environment and shows the possible reduction of production costs and fish meal dependence.