We investigated the effects of compost (CM), made from poultry and cattle manure with spent mushroom substrate, plus chemical fertilizers (CFs) on soil organic carbon (C) and nitrogen (N) fractions in silty loam soil of the Loess Plateau. Eight fertilizer practices were applied in a 7‐year‐old ‘Red Fuji’ apple (Malus domestica Borkh.) orchard for 360 days. Compared to CM alone, CM–CFs decreased slightly soil total organic C but increased total N by 4.3–11.6%. Notably, CM–CFs increased soil microbial biomass C (MBC) by 2.7–26.5% and microbial biomass N (MBN) by 7–13.7%. Soil water‐soluble carbon (WSC) was increased by 20.7% and 19.2% when 2% CM plus N and phosphorus (P) (2%M–NP) and 4% CM plus N and P (4%M–NP) were applied, respectively. Whereas 0.5% CM plus N and P (0.5%M–NP) increased WSC by 9.3% on day 30 but decreased it by 7.2% from 30–360 days. Hot water‐soluble C increased by 13.1–14.6% from 0–180 day, but thereafter, the effect disappeared. Compared to CFs, CM–CFs increased MBN by 35.1–115.6%, and increased alkali‐hydrolyzable‐N by 3.5–55.8% over 180–360 days of incubation. Additionally, CM–CFs promoted N mineralization, increasing NH4‐N and NO3‐N contents. Based on the changes in C and N fractions and available nutrients, 2%M–NP (45 t/ha of CM plus 450 kg/ha of N and 157.5 kg/ha of P) may be the optimal fertilizer strategy for stimulating soil microbial growth and activity, and enhancing nutrient cycling for apple growth.