Display omitted •ZrO2-CaCr2O4-BiOIO3 nanocomposite were synthesised by facile co-precipitation method.•The NCs exhibits excellent photodegradation of cefixime and doxycycline.•The end product toxicity was evaluated against E.coli and S.epidermis.•Investigation of genotoxicity towards Allium cepa.•Elucidation of photodegradation pathway using ECOSAR software. Today, diverse form of antibiotic drugs has been used extensively for the treatment of various microbe related diseases. The improper handling and overusage of these antibiotics have tremendously affected the aquatic system. Therefore, the development of low cost and highly efficient photocatalyst for the effective degradation of antibiotics is paramount for the remediation of toxic pollutants in water bodies. In the present study, the ternary ZrO2-CaCr2O4-BiOIO3 nanocomposite (NC) has been newly fabricated under simple chemical co-precipitation technique. The developed ternary NC was investigated for the photodegradation of cefixime (CFX) and doxycycline (DOX) under visible light irradiation. The prepared NC was characterized by various physiochemical analysis including HR-TEM, SEM, UV–vis DRS, XPS, FT-IR, ESR, PL, Raman, EIS, and N2 adsorption and desorption analysis. The reusability of the photocatalyst was tested by performing six consecutive cycles. The toxicity of the degraded end products of CFX and DOX has been evaluated against E. coli and S. epidermis. The fabricated NC was investigated for its photodegradation efficiency under different parameters such as pH, antibiotic concentration, and NC dosage. The photodegradation mechanism was elucidated using scavenging study, and ESR analysis. The TOC results confirmed the complete mineralisation of CFX and DOX. Also, the possible degradation pathway of CFX and DOX was determined based on GC–MS analysis. The fabricated NC were investigated for the genotoxicity towards Allium cepa. The present study opens up a new insight for using ZrO2-CaCr2O4-BiOIO3 photocatalyst for remediation of pharmaceutical pollutant.