Vehicular air pollution is a mounting health issue of the modern age, particularly in urban populations of the developing nations. Auto-rickshaws are not considered eco-friendly as to their inefficient engines producing large amount of particulate matter (PM), thus posing significant environmental threat. The present study was conducted to ascertain the cytotoxic, phytotoxic, and mutagenic potential of PM from gasoline-powered two-stroke auto-rickshaws (TSA) and compressed natural gas-powered four-stroke auto-rickshaws (FSA). Based on the increased amount of aluminum quantified during proton-induced X-ray emission analysis of PM from TSA and FSA, different concentrations of aluminum sulfate were also tested to determine its eco-toxicological potential. The MTT assay demonstrated significant (p < 0.001) dose-dependent cytotoxic effects of different concentrations of TSA, FSA, and aluminum sulfate on BHK-21 cell line. LC50 of TSA, FSA, and aluminum sulfate was quantified at 16, 11, and 23.8 μg/ml, respectively, establishing PM from FSA, a highly cytotoxic material. In case of phytotoxicity screening using Zea mays, the results demonstrated that all three tested materials were equally phytotoxic at higher concentrations producing significant reduction (p < 0.001) in seed germination. Aluminum sulfate proved to be a highly phytotoxic agent even at its lowest concentration. Mutagenicity was assessed by fluctuation Salmonella reverse mutation assay adopting TA100 and TA98 mutant strains with (+S9) and without (-S9) metabolic activation. Despite the fact that different concentrations of PM from both sources, i.e., TSA and FSA were highly mutagenic (p < 0.001) even at lower concentrations, the mutagenic index was higher in TSA. Data advocate that all tested materials are equally ecotoxic, and if the existing trend of atmospheric pollution by auto-rickshaws is continued, airborne heavy metals will seriously affect the normal growth of local inhabitants and increased contamination of agricultural products, which will amplify the dietary intake of the toxic elements and could result in genetic mutation or long-term health implications.