Both atmospheric nitrogen (N) deposition and biochar application can markedly impact soil heterotrophic respiration (RH), an important component of the global carbon cycle. However, the interactive effects of N deposition and biochar application on soil RH in subtropical forest ecosystems remain unclear. Here, we conducted a three-year (2019–2022) field trial within a bamboo forest in subtropical China to examine the responses of soil physicochemical and microbial properties to N deposition and biochar application, and to elucidate how biochar regulates N deposition-induced change in soil RH. Nitrogen deposition stimulated soil RH by 8.1–9.8 % annually over three years compared to the control, and this stimulation was mitigated (by 8.1–8.9 % annually) with biochar addition. In the context of N deposition, the decrease of soil RH by biochar application was not through changing soil temperature, moisture or labile organic carbon content. Biochar treatment reduced the abundances of bacterial glycoside hydrolase family 48 gene (GH48) and fungal glycoside hydrolase family 7 cellobiohydrolase I gene (cbhI) and the activities of β-glucosidase and cellobiohydrolase (CBH), but increased the abundance of cbbL gene and activity of RubisCO enzyme. Furthermore, the RH was correlated positively (P < 0.01) with β-glucosidase and CBH activities and negatively (P < 0.01) with RubisCO enzyme activity. Structural equation modeling revealed that the biochar-induced reduction of soil RH under N deposition was associated with decreases in the abundance of cbhI gene and the activity of CBH in soils. We highlight that management practices can mitigate soil carbon loss in forests through modulating soil microbial functions under atmospheric N deposition, and that biochar application in Moso bamboo forests has the potential to reduce RH by approximately 7.6 × 106 t CO2 yr−1 under atmospheric N deposition.