Tomato fruit enormously consumed in Burkina Faso is a source of health risk due to its quality. The plant of tomato cultivated in most the industrially polluted area as Ouagadougou, accumulates significant quantities of heavy metals and microorganisms and could be dangerous for consumption. The present study was conducted to investigate heavy metal and microbial contamination in soils wastewater and vegetables (tomato fruit) and to evaluate the possible health risks associated with the consumption of vegetables. Total concentrations of As, Cd, Cr, Cu, Hg, Ni, Se and Zn were determined using atomic absorption spectrophotometry. Transfer factor (TF), daily intake of metals (DIM) and health risk index (HRI) were also calculated. Microbial quality was analyzed for the presence of foodborne pathogens. The pH involved from 6.50 ± 0.1 to 9.40 ± 0.12 respectively for Boulmiougou and Kossodo. The mean metal concentrations indicated that soils were strongly polluted followed by wastewater and vegetable. The range of the mean values (in mg·kg −1 ) exhibited by As, Cd, Cr, Cu, Hg, Ni, Se and Zn in tomato fruit was 17.