Dietary aflatoxins are a major risk to the health of aquaculture species and their animal and human consumers. This study reports a first comparative antitoxic and antifungal activity of natural probiotic (honey) and antifungal drug (natamycin)-supplemented diets to alleviate the toxicity induced by the fungus (A. flavus) or it’s producing aflatoxins. A set of experiments were primarily conducted in vitro including determining the minimum inhibitory concentration (MIC) of A. flavus for natamycin and honey and the antifungal activity of the honey, besides contaminating a fish diet with toxigenic strain A. flavus then detecting the dietary presence of aflatoxins, using TLC, before and after cultivating the fungus. We further investigated the influence of honey and natamycin on growth; biochemical parameters; histology and immunohistochemistry; and liver residual deposition (using HPLC to identify the aflatoxin type and amount). One hundred and eighty Nile tilapia (Oreochromis niloticus) (25.99 ± 3.31 g) were allocated into six groups in triplicates (10 fish/replicate). A control group (G1) and five other groups, G2, G3, G4, G5, and G6, were fed daily a basal diet and basal diets enriched with honey (70% concentration, 200 ml kgL− 1 diet)) (H), natamycin (2.5 g kgL− 1 ) (N), aflatoxins, and combined aflatoxins groups (aflatoxins+H and aflatoxins+N) respectively for 45 days. Fish received aflatoxins-contaminated diet (G4) showed low growth, and alterations in immune status, hepatic antioxidant, and hepato-renal biomarkers. Additionally, it revealed histological changes in liver and kidneys tissues, besides a strong caspase-3 and weak BCL-2 immunohistoreactivity compared to combined groups (G5, G6), and higher tissues bioaccumulation. The dietary additive of honey (G2) significantly (P < 0.05) elevated growth parameters; serum immunological biomarkers including lysozyme, nitric oxide (NO), and Myeloperoxidase (MPO); tissue antioxidant indicators including superoxide dismutase (SOD) and reduced glutathione (GSH) implying oxidative protection; and retrieved the malondialdehyde (MDA), antistress indicator (cortisol), hepato-renal parameters including ALP, AST, ALT, urea, creatinine. At the tissue and cellular level, honey sustained the histological architecture, modulated the immunohistochemical parameters, and efficiently mitigated the aflatoxins residual deposition in hepatic tissues compared to natamycin (G3) and control (G1). Comparing the antitoxic efficiency of honey and natamycin for the supplemented groups with aflatoxins (G5 and G6), natamycin was more effective in Amelio-rating the toxicity with aflatoxins reflected in modulating all measured parameters and low mortalities compared to honey. The dietary additive of natamycin had the ability to eliminate aflatoxin B1 and reduced the amount of aflatoxin G1, while honey eliminated aflatoxin G1 and decreased the aflatoxin B1 level. From the study out-comes, and to overcome the usage of antifungal drugs, the dietary additive of honey is a research hotspot both for the beneficial impacts including growth promoter, immune stimulator, hepatic antioxidant protection, tissue architecture maintaining, and aflatoxins detoxification in O. niloticus, and as a safe alternative to the antifungal drug.