Increased nitrogen (N) deposition endangers the biodiversity and stability of forest ecosystems, and much of the original phosphorus (P) parent material continues to decrease in most lowland tropical forests. It remains poorly understood as to how soil microbial diversity at a molecular level responds to the addition of excess N and mitigation of soil P limitation, as well as their influencing factors, in the N-rich tropical forest ecosystems. To reach a better understanding, we conducted a six-year N and P-addition experiment consisting of three treatments: N-addition (150 kg N ha−1 yr−1), P-addition (150 kg P ha−1 yr−1), and NP-addition (150 kg N ha−1 yr−1 plus 150 kg P ha−1 yr−1), besides a control treatment in an old-growth tropical forest in southern China. We examined the snapshot responses of soil bacterial richness and community composition to the elevated N and P levels after six years using a 16S rRNA gene MiSeq sequencing method. The soil bacterial α-diversity, which is represented by Chao1 index in terms of bacterial richness, was 783 ± 87 (mean ± SD) across all samples in this study. The N addition caused a decline in soil bacterial richness, most likely through its negative effect on soil pH. The decrease in soil pH resulted from the direct N input and indirect NO3− increase. However, the P treatment had no effect on soil bacterial richness. The NP treatment also reduced the soil bacterial richness as the N addition. These results suggested that the P input could not alleviate the loss of soil bacterial richness induced by excess N deposition in the old-growth N-rich tropical forest. The Acidobacteria, which comprised 31.1% of the soil bacterial community, were the most dominant bacteria across all samples. The addition of P shifted the soil bacterial community composition. The elevated P availability with P-addition and the decreased understory plant coverage in the N-input treatment altered the soil bacterial β-diversity. Our results highlight the different roles of N and P depositions in shaping the soil bacterial richness and community composition, thereby causing concomitant changes in understory plant and underground microbial communities in this ecosystem. •A decrease in soil pH resulted from the direct N input and indirect NO3− increase.•N addition caused a decline in bacterial richness, possibly through its effect on pH.•Phosphorus addition shifted the soil bacterial community composition.•Elevated P availability and lower understory coverage altered bacterial community.•N and P additions play different roles in shaping bacterial richness and community.