Application of organic amendments (OAs) combined with inorganic fertilizers or gypsum in poorly structured soils has recently received much attention as an agricultural management practice aiming to ameliorate physicochemical constraints and improving soil carbon (C) storage. Although microbial C-use efficiency (CUE) is recognized as a critical parameter in ecological models to predict soil C cycling and storage, little is known about the effects of OAs with exogenous nutrient supply (to balance the resource nutrient stoichiometry) or gypsum on microbial biomass and CUE. Here, we examined the role of OAs (C4 vegetation-derived: δ13C – 12 to − 15‰) in altering microbial biomass, C mineralization, and CUE, i.e., microbial growth relative to microbial C uptake (microbial growth + respiration + death) over the long-term, in an alkaline sodic-subsoil (C3 vegetation-derived: δ13C – 24‰). Four different OAs (sorghum stubble, sugarcane bagasse, sugarcane mill mud, and sugarcane mill mud + sugarcane mill ash) were used at 6.2 g C kg−1 soil, with and without the exogenous supply of nutrients and/or gypsum. The nutrients were added with the aim to convert OAs to stable soil organic matter (SOM) with a C/nitrogen (N)/phosphorus (P) stoichiometric ratio of 100:8.3:2. Over 90 days, the cumulative mineralization of OA-C varied across OA types and ranged between 42 and 497 mg CO2-C g−1 OA-C. The OA-derived microbial biomass C (MBC) ranged between 20 and 350 mg C kg−1 soil across the treatments, which was highest with sorghum stubble that contained the highest dissolved (labile) organic C. The mill mud with an inherently balanced C/nutrient stoichiometry had the highest CUE, i.e., 0.3–0.8, compared to the sorghum stubble and sugarcane bagasse (with imbalanced nutrient stoichiometry), i.e., 0.1–0.6. Balancing the nutrient stoichiometry of sorghum stubble and sugarcane bagasse via nutrient inputs increased MBC but not CUE. The input of gypsum to the OA-treated soil had no impact on either MBC or CUE. In conclusion, balanced C/nutrient stoichiometry and labile C content of OAs are critical properties to control their impact on C mineralization, MBC, and CUE, with implications for soil C storage upon amendment into a poorly structured sodic-subsoil.