In latest years, various techniques and chemicals have been used for the control of microbial influenced corrosion (MIC) of metals. The application of botanical-based biocides is one of the effective and practical techniques in the fight against MIC. In the present study, the role of aqueous extract of ginger (Zingiber officinale) (GIE) as green biocide to control MIC of mild steel 1010 (MS) in a cooling water system was investigated. Biocorrosion behavior of Bacillus thuringiensis EN2 on MS and its control by GIE was analyzed by electrochemical measurements. Polarization, electrochemical studies (ES), weight loss measurements (WL), and surface analysis (XRD, X-ray diffraction spectroscopy, and FTIR, Fourier transform infra-red spectroscopy) were performed under various incubation periods up to 4 weeks. We observed that EN2 forms a thick biofilm on the MS metal surface at the end of the incubation period and the WL significantly increased to 993 mg at fourth week when compared to the initial immersion period (194 ± 2 mg). In contrast, with addition of GIE, WL was reduced about 41 ± 2 mg over biotic system (993 ± 2 mg). GC–MS analysis confirmed the adsorption of active component of GIE (β-turmerone) on the metal surface as a protective layer to prevent the biofilm formation and thus leads to reduction of corrosion. The optimum 20 ppm of GIE was found to be effective corrosion inhibition efficiency which was about 80%. From the results of WL, ES, XRD, FTIR, and GC–MS, GIE was identified as biocide and thus inhibits the bacterial growth on MS metal surface and it leads to control MIC. XRD showed that the GIE with EN2 resulted in less formation of corrosion products over biotic and abiotic systems. Overall, this research first shed light on the antibacterial activity of GIE inhibiting biofilm formation, thus reducing the corrosion of MS in cooling water systems.