The success of the biofloc system is contingent on its management. Therefore, this study seeked to assess the effects of intermittent fasting at different feeding rates on the efficacy of the biofloc system in terms of water quality, floc composition, growth performance, muscular chemical composition, and histomorphometry changes in the Nile tilapia muscles in comparison to the traditional system. A total of six hundred Nile tilapia fingerlings (with an average initial body weight of 54.19±1.32g) were divided into five treatments: T0 (the control) consisted of fish reared in the traditional system and fed at a rate of 4% of their body weight (BW). While, in treatments T1 and T2, fish received a feeding rate of 3% of their body weight, with T1 being subjected to continuous feeding and T2 experiencing intermittent fasting (alternating between a feeding day and a fasting day). Likewise, T3 and T4 fish were fed at a rate of 4% of their BW and were exposed to continuous feeding and intermittent fasting, respectively. The average quantity of floc, total bacteria in the floc, total phytoplankton, and total zooplankton increased with increasing feeding rates but decreased when subjected to intermittent fasting. Fish in the biofloc-based treatments exhibited superior growth performance and feed efficiency parameters when compared to those reared in the traditional system. Among the treatments, fish in T3 demonstrated the highest levels of moisture, fat, and energy content while displaying the lowest levels of protein and ash contents among other treatments. Fish in treatment T2 exhibited the lowest values of large and mean diameters and the highest values of muscular bundle intensity in comparison to the other treatments. Finally, these findings support the efficacy of intermittent fasting as a viable approach to biofloc system management, as it results in a noteworthy decrease in aquafeed expenses and overall fish production.