The present study assessed the accumulation and distribution of metals in tomato (Lycopersicon esculentum L.) fruits grown with wastewater. The concentrations of nine metals (Co, Cd, Mn, Cu, Ni, Fe, Zn, and Pb) were analyzed in wastewater collected from the study site. Four metals with substantially higher concentrations in wastewater, namely Fe, Zn, Mn, and Pb, were selected for further analysis in soil, plant organs, and parts of tomato fruits. In addition, the concentrations of essential nutrients (Na, K, Ca, P, and N) in all samples were also analyzed. Concentrations of Zn (0.77 mg L−1) and Pb (0.44 mg L−1) were found to be the maximum, and Mn concentration was the minimum (0.16 mg L−1) in wastewater samples. However, in soil samples, the concentrations of Fe (35.88 mg kg−1) and Pb (29.62 mg kg−1) were the highest, which ultimately led to their higher accumulation in plant tissues. When metal accumulation in the whole plant and tomato fruit was compared with the WHO permissible limits, the accumulated concentrations of Zn (16.35, 12.98, and 23.85 mg kg−1 d.wt. in peri-, endo-, and mesocarp, respectively), Mn (7.08, 7.75, and 4.6 mg kg−1 d.wt. in peri-, endo-, and mesocarp, respectively), and Pb (30.05, 29.42, and 34.95 mg kg−1 d.wt. in peri-, endo-, and mesocarp, respectively) exceeded the safe limits except for Fe (13.6, 32.3, and 63.43 mg kg−1 d.wt. in peri-, endo-, and mesocarp, respectively). Thus, the irrigation of tomato fruits with wastewater can cause health risks to humans under prolonged consumption, and the regular monitoring of metals is necessary to reduce the health risks from human consumption.