SUMMARYAmendments of nutrient‐deficient soil with three organic manures and one non‐edible oil‐cake reduced the disease controlling potential of methoxyethyl mercury chloride (MEMC), quintozene and carbendazim used as seed treatments on cowpea and cotton against seedling rot caused by Rhizoctonia solani.Biogas sludge (BGS) and farm yard manure (FYM) nullified the activity of MEMC and quintozene and reduced markedly the efficacy of carbendazim. Humic acid extracted from BGS inactivated MEMC and carbendazim but had little effect on quintozene. Green manure (Sesbania aculeata) slightly reduced the efficacy of MEMC only. Soil amendment with mahua (Madhuca indica) cake and soil drench with its aqueous extract greatly reduced the efficacy of the three fungicides.