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Although returning crop residue to fields is a recommended measure for improving soil carbon (C) stocks in agroecosystems, the response of newly formed soil C (NFC) to the integrated supply of residue and nutrients and the microbial mechanisms involved in NFC are not fully understood. Therefore, an 84-day incubation experiment was conducted to ascertain the microbial mechanisms that underpin the NFC response to inputs of residue and nitrogen (N), phosphorus (P), and sulfur (S) in two black (Phaeozem) soils from experimental plots at Gongzhuling, Jilin Province and Hailun, Heilongjiang Province, China. The results showed that adding residue alone accelerated microbial nutrient mining, which was supported by decreases of 8–16% in the ratios of C:N and C:P enzyme activities, relative to soils with nutrient inputs. The NFC amounts increased from 1 156 to 1 722 mg kg−1 in Gongzhuling soil and from 725 to 1 067 mg kg−1 in Hailun soil as the levels of nutrient supplementation increased. Boosted regression tree analysis suggested that β-glucosidase (BG), acid phosphatase (AP), microbial biomass C (MBC), and Acidobacteria accounted for 27.8, 18.5, 14.7, and 8.1%, respectively, of the NFC in Gongzhuling soil and for 25.9, 29.5, 10.1, and 13.9%, respectively, of the NFC in Hailun soil. Path analysis determined that Acidobacteria positively influenced NFC both directly and indirectly by regulating BG, AP, and MBC, in which MBC acquisition was regulated more by AP. The amount of NFC was lower in Hailun soil than in Gongzhuling soil and was directly affected by AP, indicating the importance of soil properties such as SOC and pH in determining NFC. Overall, our results reveal the response of NFC to supplementation by N, P, and S, which depends on Acidobacteria and Proteobacteria, and their investment in BG and AP in residue-amended soil.