Fungi and bacteria play a central role in the cycling of carbon (C) and nitrogen (N), which has been frequently assessed by manipulating their abundance in soil with the application of fungicides and bactericides. We conducted a meta-analysis using 61 publications to investigate whether fungicides and bactericides have distinct effects on soil C- and N- cycling, and how they vary with land type and soil properties. Most fungicides and bactericides had significant negative effects on microbial biomass C and N. However, they had mixed effects on soil respiration, N pools, and transformation processes, varying strongly with the type of fungicide and bactericide. Available NO3− was lightly affected, while N2O emission was reduced by most biocides. The application of fungicides had neutral effects on respiration, NH4+, and ammonification in agro-ecosystems, but positive effects in forests. Effect sizes of available NO3− and nitrification in response to bactericides were sensitive to soil pH and C content. Our results suggest that most fungicides and bactericides inhibit microbial growth, but that they have mixed effects on respiration and N cycling. Biocides need to be carefully evaluated for unintentional side effects before they are used in assessing the role of fungi and bacteria for C- and N- cycling.