Organotin compounds are applied in several industrial reactions and can present antifungal and antibacterial activities. Incorrect handling and storage practices of biodiesel and diesel-biodiesel blends can lead to microbial development, impacting its final quality. Concerning this problem, this work investigated the antimicrobial action of two organotin catalysts used in biodiesel production with four isolated microroorganisms (Bacillus pumilus, Pseudomonas aeruginosa, Pseudallescheria boydii, and Aureobasidium pullulans) and a pool of microorganisms (ASTM E1259 standard practice). Samples of soybean biodiesel with different concentrations of dibutyl tin dilaurate (catalyst 1) and di-n-butyl-oxo-stannane (catalyst 2) were prepared and added of mineral medium. The pool of microorganisms was inoculated and incubated at 30 °C and final biomass was weighted after 14 days. Thereafter, soybean biodiesel with catalyst 2 was used. Fungal biomass was weighted, and plate count was used to assess bacterial growth. Results show that catalysts 1 and 2 presented no inhibitory activity on the pool of microorganisms evaluated. A slight inhibitory activity was observed for B. pumilus and A. pullulans growth, but not for P. boydii, P. aeruginosa, or the pool of microorganisms. All experiment exhibited acidification higher than sterile control. Infrared analysis show less microbiological degradation products in the tin-protected fuel with ASTM inoculum. These results suggest that these tin-based catalysts show no toxic effect on native microbial population and a slight effect on some isolated microbial population in laboratory scale and for the first time shows that these organotin compounds can be employed safely as biodiesel catalyst. Graphical abstract.