Spent mushroom substrates can be utilized as organic fertilizer in agricultural production but may pose a health risk. Nitrification inhibitors dicyandiamide and 3,4-dimethylpyrazole phosphate have been used to enhance fertilizer nitrogen utilization efficiency. However, the changes of soil abiotic properties, microbial activities, nitrogen cycling and human-disease genes, and their comprehensive relationships after the spent mushroom substrate and nitrification inhibitor applications were still unknown. In this study, the spent mushroom substrate and nitrification inhibitor were applied into the agricultural soils at the rates of 2.5% (w/w) and 1.0% of nitrogen content in the spent mushroom substrate, respectively, and then lettuce was planted. Compared with the control, spent mushroom substrate application significantly increased the lettuce biomass, soil enzyme activities and chitinase, protease, nitric-oxide reductase, nitrogenase, and urease gene abundances. However, the antibiotic resistance and human-disease gene abundances were also significantly enhanced following the spent mushroom substrate application. Relative to spent mushroom substrate alone, the dicyandiamide application significantly decreased the soil pH and human-disease gene abundances, although extra dicyandiamide and 3,4-dimethylpyrazole phosphate enhanced 61.4% and 45.0% of dry biomass of aboveground lettuce. The human-disease gene abundances were positively correlated with soil pH but were negatively correlated with the Acidobacteria and Streptomyces ratios in soils. Spent mushroom substrate application could generate double-edged sword effects, and the health risk should be considered in the spent mushroom substrate applications. Extra dicyandiamide application could further promote crop growth while decrease the human-disease risk from the spent mushroom substrate.