Microbiologically influenced corrosion (MIC) is a phenomenon that contributes to the deterioration of metallic materials in industrial environments. This process has a significant impact on the infrastructure of oilfields, primarily affecting pipelines, storage tanks, and water distribution systems. The main bacterial groups associated with biocorrosion can be classified based on the metabolic pathways they employ. These include sulfate-reducing bacteria (SRB), acid-producing bacteria (APB), and thiosulfate-reducing bacteria (TRB), among others, which colonize and degrade metal surfaces through various metabolic mechanisms. This study aimed to evaluate the efficacy of different biocidal compounds in controlling TRB under laboratory conditions. The modified Time Kill Test (TKT) technique was employed using special BioCIC liquid culture media from the Corporación para la Investigación de la Corrosión (CIC). Seven biocide treatments were tested, including formulations based on tetrakis (hydroxymethyl) phosphonium sulfate (THPS), quaternary ammonium, and glutaraldehyde, among others. Bacterial incubation was conducted at 70°C for 28 days to simulate field conditions. To identify microorganisms associated with biocorrosion in the production water at a Colombian oilfield, total genomic DNA was extracted from the samples and sequenced using the Oxford Nanopore Technology. Among the tested treatments, the M1 formulation (quaternary ammonium 10–30%, THPS 10–30%, and glutaraldehyde 10–30%) exhibited the highest antimicrobial efficacy, significantly reducing bacterial growth compared to the other biocides. The molecular identification of microbial communities in production water samples from seven different field locations revealed Thermotoga and Thermovirga as the predominant genera. However, post-TKT cultures treated with M1 showed a shift in microbial composition, with Acetomicrobium emerging as the dominant genus. These findings highlight the importance of evaluating diverse biocidal formulations to optimize MIC control strategies. Additionally, characterizing microbial populations in production waters is crucial for developing targeted mitigation approaches tailored to the specific microbial consortia present in each field.