Microbiologically influenced corrosion (MIC), primarily caused by sulfate-reducing bacteria (SRB) biofilms, presents a significant challenge to the integrity of petroleum pipeline systems. In this study, zinc oxide nanoparticles (ZnO NPs) were green-synthesized using tomato peel extract and evaluated for their corrosion inhibition performance in anaerobic conditions. The presence of phytochemicals in the extract facilitated the formation of hexagonal wurtzite-structured ZnO NPs (with a size range of 20–45 nm) with organic-inorganic hybrid interfaces, enhancing their interfacial interaction and anti-biofilm capability. Surface-bound biomolecules rapidly adsorbed onto the metal surface, forming a transient passivation layer that effectively suppressed early-stage corrosion by retarding initial anodic dissolution. The green-synthesized ZnO NPs achieved a 90.6% reduction in viable SRB cells, reduced corrosion rate by 74.2% (based on weight loss), decreased corrosion pit depth by 83.9% (via 3D profilometry), and inhibited biofilm formation by 67.5% (quantified by CLSM). Electrochemical impedance spectroscopy further showed that the green ZnO NPs increased charge-transfer resistance by approximately 13 times and 11 times after 7 and 28 days, respectively, outperforming chemically synthesized ZnO NPs by about 7.8 times. The enhanced electrochemical performance, combined with the sustainable origin derived from agricultural waste and the environmental friendliness of the synthesis process, underscores the potential of tomato peel-derived ZnO NPs as an efficient and eco-friendly alternative for MIC mitigation in oilfield pipeline systems.