A 12-week study was conducted to investigate the effects of the addition of probiotic (Bacillus spp.)on water quality, production performance, microbial profile, and food quality of the Nile tilapia (Oreochromis niloticus) and mint (Mentha Spicata) in a combined aquaponic system. The Nile tilapia fingerlings with an initial body weight of 10g were stocked at 80 fish/m3. Each hydroponic system was composed of 36 mint seedlings with an initial length of 3.65 ± 0.09 cm. Two treatments with three replicates were designed: the 1st with probiotic addition (W/ Pro) and the 2nd without probiotic addition (W/O Pro). Increased dissolved oxygen concentration was observed in the control group (5.43 ± 0.07 mg/l). NH3 and NO2 were significantly lower in W/ Pro treatment (0.03 ± 0.00 and 0.46 ± 0.01 mg/l) than the control (0.04 ± 0.00 and 0.51 ± 0.02 mg/l). Final body weight, weight gain, average daily weight gain, and specific growth rate (38.14± 1.41, 28.15 ± 1.41. 0.33 ± 0.01, and 2.34 ± 0.11, respectively) were significantly improved with the W/ Pro treatment. The survival rate% was higher in W/ Pro treatment without significant differences. A better feed conversion ratio was obtained in the W/ Pro treatment (1.41 ± 0.05) compared to (1.65 ± 0.05) in the W/O Pro systems. Plant fresh weight and length at harvest were better in W/Pro, while moisture content was significantly higher in W/O Pro ones. Adding probiotics increased the total bacterial counts in fish, water and mint. Bacteria that are considered a potential risk of seafood-borne infection including Bacillus cereus were only identified in fish of the control. Similarly, pathogenic Aeromonas hydrophila and Acinetobacter baumannii were associated with water and mint from the control. Adding probiotics promoted the growth of beneficial lactic acid bacteria, Bacillus lecheniformis, prevented the pathogenic ones and did not affect the presence of Rahnella aquatilis bacteria.