Soil infertility is a significant challenge in achieving sustainable agricultural practices. In this regard, the chemical fertilizer usage is not an environmentally friendly solution. Organic amendment and bacterial inoculation can positively restore soil quality, enhancing biogeochemical nutrient cycles. In this study, we assessed the effect of adding plant growth-promoting bacteria (PGPB) alongside organic amendments on the physicochemical parameters of sandy-loam soils. Over a 90-day pot experiment, we measured organic matter accumulation, physicochemical, chemical variation trends and changes in microbial community assemblages. Working on the joint application could have a synergistic effect; different agro wastes spent such as mushroom substrate (SMS), empty fruit bunch (EFB) of palm oil and pineapple leaf (PL) residue was amended with Paenibacillus polymyxa ATCC 825 and effective microorganism. Significant changes in soil properties (physicochemical and microbial community) due to the application of P. polymyxa and SMS-amended material were observed after incubation. On average, an increase in water holding capacity, soil pH and mineral content availability was significantly higher than other amended materials. Compared to others, the organic amendment significantly increased sandy-soil aggregation content by 44%. In addition, increased taxonomic diversity in phyla composition was observed with an abundance of Proteobacteria (33%), Firmicutes (18%), Actinobacteria (14%), Bacteriodata (12%), and Verrucomicrobia (6%). The findings indicate that the addition of SMS amendment with bacterial inoculation is beneficial for problematic soil recovery. The incorporation of bacterial inoculation, specifically P. polymyxa ATCC 825, following organic amendment, seems to have a greater positive effect on the soil characteristics.