Malachite green (MG) dye, besides coloring is used as an effective aquaculture therapeutic. The present study assesses the mitigating ability of Emblica officinalis (EO) fruit extract against the dye induced chronic (60 days) cyto-toxicity in Cyprinus carpio. For this, four experimental groups were maintained: group I—control, group II—MG, group III—EO (positive control), group IV—MG + EO. The study was made at three tiers: detailing structural anomalies using a light microscope and transmission electron microscope (TEM), biochemical estimation of antioxidant enzymes, and lipid peroxidation and molecular analysis of expression patterns of HSP70, and CYP1A genes. MG intoxication resulted in necrosis, cytoplasmic vacuolation, glycogen depletion, abundant macrophages, loss of cell integrity and prominent nuclear alterations. Significant (p < 0.05) inhibition in the activities of catalase (CAT), superoxide dismutase (SOD), glutathione-S-transferase (GST) and reduced glutathione (GSH), along with an elevation in malondialdehyde (MDA) levels, occurred after 60 days of MG exposure. CYP1A and HSP70 genes presented a significant change in their expression in MG treated fish. Whereas oral supplementation with EO significantly restored the histo-architecture, normalized the altered enzymatic activity, reduced the oxidative stress level and downregulated the expression of HSP70 and CYP1A genes. Thus, it can be concluded that EO acted as an effective ameliorant against malachite green induced cyto-toxicity in Cyprinus carpio.