This research introduces a pioneering biogenic deposition-precipitation method for synthesis of Ag@g-C3N4 nanocomposites (NCs) employing fennel seed extract (FSE). This technique involves the reduction and capping of silver nanoparticles (AgNPs) onto g-C3N4, employing polyphenolic content of FSE, consequently establishing a strong Schottky junction. The, NCs were characterized through various spectroscopic and microscopic techniques, confirming successful biogenic deposition of AgNPs and purity of prepared nanomaterials. Further, the synthesized NCs were utilized for photocatalytic degradation of various hazardous pollutants viz. Rhodamine-B (Rh-B) dye, Tetracycline (TCy) antibiotic, Imidacloprid (IMD) insecticide and deactivation of E. coli microbes. Amongst the synthesized NCs, 3 wt% Ag@g-C3N4 NCs exhibited superior photocatalytic mitigation of Rh-B (99.26%, k = 90.4 × 10−3 min−1), TCy (96.86%, k = 40.2 × 10−3 min−1), IMD (95.7%, k = 34.96 × 10−3 min−1) and E. coli deactivation (99.5%, k = 49.19 × 10−3 min−1). Moreover, the rate constants revealed many-fold increase in photocatalytic degradation of pollutants, contrary to pristine g-C3N4 (k = 11.8 × 10−3 min−1). This investigation also unveils an intricate photocatalytic mitigation pathway for the aforementioned-contaminants, elucidating key role of superoxide radical anions in photocatalytic mitigation. One of the significant highlights of this research is the sustainable and cost-effective synthesis methodology involving fennel seeds, which not only ensures the wide availability of resources but also guarantees environmental safety, in alignment with green principles.