Monoammonium phosphate is a commonly used fertilizer for better crop production. However, its repeated application causes the accumulation of harmful metals levels in plants and soil over time. Here, the impact of the purification of monoammonium phosphate fertilizer on vegetative growth and yield of tomato plants (Lycopersicon esculentum L.), and the heavy metals accumulation in both soil mix and tomato fruits was investigated through a pot experiment on three different concentrations of purified and unpurified monoammonium phosphate fertilizer. This study showed that the purification of monoammonium phosphate led to a significant enhancement on vegetative growth and yield attributes, mainly for 1 g/L of purified fertilizer. Importantly, the physicochemical investigations showed a significant reduction in heavy metals accumulation (Pb, Cr, Cd, Ni, and V) in the fruits and the soil mix treated with purified monoammonium phosphate. This study confirms that the use of purified monoammonium phosphate fertilizer improves the fruit yield and at the same time reduces the impact of toxicity of heavy metals present in the environment, which can be classified as a part of an environmental management systems.