Mechanisms of action attributed to feed additives are of continuous research interest, increasing our knowledge about the side effects (direct or indirect) of their application. The primary role of organically modified clinoptilolite is to bind multiple polar and non-polar mycotoxins contaminating the feed and remove them during the digestion process and through feces, therefore preventing adsorption and consequences of mycotoxicosis on fish health. However, it is not fully understood if this binding action can influence bacterial communities in the fish digestive tract and possibly other organs, as well as the aquatic environment. Therefore, in this study, Nile tilapias (Oreochromis niloticus) (average weight: 30 ± 2 g; n = 48) were simultaneously exposed to low-level mycotoxins (AFB1 40 µg/kg, FB 600 µg/kg, ZEN 50 µg/kg, and DON 150 µg/kg) added to diet, with and without supplementation of commercially available organically modified clinoptilolite feed additive (MinazelPlus^®, 2 g/kg). After 42 days of continuous exposure, gill tissue, feces, and water were collected, and DNA was extracted from the samples. Results of RT-PCR analysis have revealed significant changes in microbiomes in fish from different groups, most prominently in mycotoxin-exposed fish. No significant changes were detected in water samples between the control and MinazelPlus^® groups, confirming the safety of MinazelPlus^® for aquatic microbial communities. MinazelPlus^® addition to the mycotoxin spiked diet, stabilized fish natural microbiota, and prevented the disbalance of microbial homeostasis observed in fish exposed to dietary mycotoxins.