Repeated annual application of paper mill biosolids (PB) and liming materials may impact soil functioning, such as nutrient cycling, organic matter decomposition, and microbial activities. The objective of this study was to evaluate the residual effect of 9 yr annual applications of PB and different liming materials on soil microbial community structure and microbial biomass C, N, and P. Treatments consisted of PB at four rates (0, 30, 60, and 90 wet Mg ha^-1), three liming by-products (calcitic lime, lime mud, and wood ash, each at 3 wet Mg ha^-1 with 30 Mg PB ha^-1), and a mineral N fertilizer surface-applied after annual crop seeding. Three years after treatment application ended, soils were sampled from 0–15 to 15–30 cm layers in each plot after corn harvest. Soil microbial community and microbial biomass C, N, and P were higher in the surface layer than deeper. Application of PB significantly increased soil microbial biomass C, N, and P and fungal biomass in both layers and induced changes in microbial community structure. In contrast, application of liming by-products did not affect microbial biomass and community. This study revealed that repeated PB application improved soil biological attributes, and those improvements can be sustained for years.