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Background Automobile repair workshops contribute immensely to the generation of soil and water contamination. This study was conducted to compare the soil microbial load, heavy metals, and consequent toxicological effects, in three (3) automobile mechanic sites. Method Soil samples were randomly collected from 3 different auto mechanic workshop in Abeokuta town of Ogun-State, Nigeria. Bacterial and fungal counts were done via standard procedures. High-performance liquid chromatography was employed for the aflatoxin quantification. Also, 24 Wistar rats were divided into 4 groups (n = 6), group 1—Control animals: orally administered distilled water, Group 2—administered soil sample solution from Ita Oshin mechanic site (I M), Group 3—administered soil sample solution from Ajebo mechanic site (A M), while Group 4—administered soil sample solution from Laderin mechanic site (L M), for two (2) weeks. Conventional methods were used to determine some physical and biochemical parameters in the rat’s serum and tissues. Results Eight bacterial and fungal genera were identified from the soil samples with Bacillus subtilis and Aspergillus niger occurring most frequently. The levels of heavy metals (lead, zinc, chromium, and cadmium) analyzed were higher than the WHO permissible heavy metal limits in all samples. The activity of liver function enzymes ALP, AST, and ALT was significantly increased in the serum of animals exposed to the 3 soil solution samples when compared with the control group, with the highest recorded at Site II. Conclusion High level of heavy metals and aflatoxins could predispose to several health-related hazards when humans are exposed to contaminated soil solutions around and within automobile mechanic areas.