Organic wastes are considered an eco-friendly fertiliser that promotes high and sustainable crop output by stimulating root development, microbiological activity, and boosting soil characteristics. Furthermore, perlite is a moisture-retentive substance incorporated into soil or plants to diminish evaporation and ensure optimal water accessibility for plant roots. The primary objective of this study was to assess the impact of synthetic and natural soil conditioners on the various chemical and physical properties of bean plants. The experiment had two soil types: sandy soil and sandy loam soil. Four concentrations of organic residues were applied: 0%, 2%, 4%, and 6%. Furthermore, two concentrations of perlite were evaluated: 0%, 0.2%, and 0.5%. The statistical analysis software SPSS was employed to analyse the results. Soil physical tests were performed, accompanied by chemical analysis of soil and vegetation. Tissues and seeds from the broad bean plant were analysed using Gas Chromatography-Mass Spectrometry (GC-MS) and High-Performance Liquid Chromatography (HPLC). The study’s findings demonstrated that a perlite concentration of 0.5% markedly enhanced the physical qualities of both soil types in comparison to the maximum concentration (6%) of organic waste. In contrast, the 6% organic wastes treatment significantly improved the chemical characteristics and nutrient content of the soil relative to the 0.2% perlite treatment for both soil types. Moreover, the HPLC and GC-MS studies indicated that the sandy loam soil containing 6% organic waste and 0.5% perlite produced the highest values regarding the type and content of phenolic and chemical components.