Residues like sewage sludge and vinasse have been reused as agricultural fertilizers, but they also present a potential to contaminate soils. Diplopods have been considered excellent bioindicators of soil contamination. In the present study, Rhinocricus padbergi were used to assess toxicity in samples of sewage sludge, biosolids, and sugarcane vinasse. The behavioral analysis, mortality rate, and histological, histochemical, and ultrastructural analyses of the midgut of diplopods were the parameters evaluated. Behaviorally, some diplopods avoided burying themselves after 30 days in soil with biosolid or vinasse. Besides, certain residue combinations were able to cause death of all individuals between 60 and 90 days of exposure. The main tissue responses were significant brush border thickening, induction of epithelial renovation, clustering of hemocytes, accumulation of cytoplasmic granules in hepatic cells, hepatic cells with heteropycnotic nuclei, and cytoplasmic degradation. Alterations were observed at various levels among treatments with different samples and exposure times. Ultrastructural analysis revealed elongation of microvilli coated with a layer of an amorphous substance, resulting in a thicker brush border as observed in the histological analysis. After 30 days of exposure, animals showed an accumulation of spherocrystals in hepatic cells and high absorption of substances, based on the elongation of microvilli. Results obtained in the chemical analysis and the behaviors observed in diplopods suggest that animals processed the residues. Therefore, caution should be exercised in the disposal of these residues in agriculture.