Purpose: Successive mineral fertilization might have side effects on soil environmental quality, such as aggregate structure, contamination, and enzyme activity. To gain a more comprehensive understanding of the influences of mineral fertilization on biotic and abiotic properties of forest soils, we investigated the effects of successive nitrogen and phosphorus fertilization on physical structures, contaminant contents, and microbial communities of forest soils with different sampling depths. Materials and methods: Mineral nitrogen (N) and phosphorus (P) were applied, alone or together, at different rates to provide nutrients to economic tree species (Chinese fir) in a forest plantation since 2011. Surface soil samples were taken at different sampling depths, and soil aggregate, contaminant content, and microbial properties were determined and comprehensively linked. Results and discussion: Our results showed that successive fertilization, sampling depths, and their interactions had negligible impacts on soil aggregate ratios and cadmium (Cd) and arsenic (As) contents. Contrastingly, soil β-glucosidase, phosphate, and fungal and actinomycetal biomass were significantly affected by the mineral fertilization, and sampling depth was a key factor determining the responses of microbial communities to the mineral fertilization. Conclusions: In the surface (0–20 cm) soils, abiotic properties had resistance to different fertilization and sampling depths, but biotic properties were markedly or significantly affected by the mineral fertilization or sampling depths. Simultaneously, sampling depths should be considered to reveal the impacts of managements on microbial properties in the surface forest soils.