Impact of soil type, soil-metal(loids) and soil-pH of rice paddies on grain-arsenic (As) and cadmium (Cd) accumulation in Malawian rice was investigated to explore the extent to which Malawi's geographical location, soil types, soil-metal(loids) and soil-pH and their interactions impact on grain-As and Cd accumulation. Multivariate techniques were used to evaluate the relationships among measured parameters. Results showed that the 1st three principal components consisting of soil-types, soil-metal(loids) and soil-pH explained 83% of total variance of both grain-As and Cd accumulation. For As, highest grain-As was detected in rice from central region (CR) cultivated in vertisols characterized with soil-As ≥ 2.5 mg/kg and soil-pH > 7.0 whereas the lowest was in rice from northern region (NR) cultivated in fluvisols characterized with soil-[As] ≤ 1.5 mg As/kg soil and soil-pH range of 6.00–6.99. For Cd, highest grain-Cd was detected in rice from CR cultivated in luvisols with soil-As range of 2.0–3.0 mg/kg and soil-pH < 6.0. For correlation, highest significant correlation coefficient was between soil-As and grain-As (0.512; p < 0.001); and soil-pH and soil-As (0.545; p < 0.001) while correlation coefficient between soil-Cd and grain-Cd and soil-Cd and grain-As were weaker and/or non-significant. These results indicate a synergy impact of soil type, soil-pH, and soil-metal(loids) that simultaneously influence low grain-As and Cd accumulation.