The presence of sulfamethoxazole (SMX) in the environment is becoming a serious problem because of its toxicity and high risk to human health and microbial activity. In this study, enhanced degradation of this compound in soil is shown by sulfamethoxazole-degrading microbes when using bagasse to pre-grow these microbial sources. The two sulfamethoxazole-degrading strains, T2 and Z3, isolated from pig manure, were selected for an immobilized microorganism technique. T2 and Z3 were identified as Enterobacter cloacae and a fungal endophyte by detailed morphological, biochemical and molecular characterization. The performance of the immobilized cells on agricultural residues (bagasse) in the biodegradation of sulfamethoxazole in soil was greater than that of cells free in solution. The effects of pH, temperature, indigenous soil microbes, and heavy metals on bioremediation were investigated, as well as the products of SMX degradation by strains, and a series of experiments at an initial concentration of 100 mg kg⁻¹ were performed at various temperatures (23–43 °C) and pHs (2.5–6.5). SMX degradation was affected by the initial temperature and pH because of the effect on the essential groups in the activation center of enzymes and membrane permeability. At 28 °C and pH 3.5, the immobilized strain T2 showed an excellent ability to degrade sulfamethoxazole in soil; 84.14% removal rate of SMX was achieved.