The increasing soil contamination by petroleum hydrocarbons has serious consequences for crop quality, eventually affecting public health and human nutrition. This study evaluates the remediation potential of bio-agents in petroleum-contaminated soil. The phytoremediation approach was facilitated by bio-absorbents (charcoal and rice husk ash, “RHA”) and bio-stimulants (plantain-based organic manure, “PBS”, algae-based organic manure, “ABS”, and seaweed extract-based organic manure, “SBS”). During the study, the total petroleum hydrocarbons (TPH), heavy metals, hydrocarbonutilizing bacteria (HUB), and hydrocarbon-utilizing fungi (HUF) levels were measured by following the recommended American Society for Testing and Materials (ASTM) guidelines. Additionally, the High-Performance Liquid Chromatography (HPLC) approach determined the tomato fruit’s nutritive qualities. The results illustrated that the appropriate combination of the treatment units substantially increased the tomato plant’s phytoremediation, dietetic, and therapeutic qualities. It was observed that the TPH phytoremediation efficiencies were lowest in the setups that used only charcoal and RHA, at 16.80 and 19.76%, respectively. Outstandingly, the bio-agents extensively increased the HUB and HUF survival, in addition to substantial increments in the fruit’s vitamin B, vitamin C, carotenoids, and phytochemical concentrations. This study’s findings underscored the prospect of utilizing sustainable agricultural materials to address environmental contamination issues and improve crop dietetic and therapeutic characteristics.