Organic fertilizer substitution offers a sustainable approach to crop production, but its impacts on plant–soil–microbial stoichiometry and rhizobacterial communities are poorly understood. A field experiment was conducted with six fertilization regimes, all fertilization treatments were designed to have equal N input: CK (control, no fertilizer), IF (chemical fertilizer), TF20, TF30, TF50 and TF100 (20%, 30%, 50% and 100% of chemical N replaced by organic fertilizer, respectively). Our results showed that compared with IF, TF20 maintained maize yield and increased nitrogen use efficiency(NUE) by 22% and plant N and P uptake by 14% and 19%. Higher substitution rates reduced phosphorus use efficiency(PUE), and 100% substitution decreased NUE by 85% and yield. However, soil total C and N concentrations and soil C:N:P ratios were unaffected by fertilization at either growth stage, indicating strong homeostatic buffering of soil C:N:P stoichiometry within one growing season. At maturity, TF20 showed an elevated microbial biomass C:P (MBC:MBP) accompanied by increased sucrase activity but no significant increase in phosphatase activity, suggesting a carbon driven stoichiometric adjustment rather than phosphorus limitation. In contrast, phosphatase activity was significantly higher under 30% and 50% substitution at maturity, indicating increased microbial phosphorus acquisition pressure at higher substitution rates. Fertilization significantly altered bacterial β-diversity at jointing, and dominant phyla correlated with plant and microbial stoichiometric ratios, suggesting community assembly driven by stoichiometry rather than soil nutrients alone. LEfSe identified distinct functional taxa enriched at different substitution rates, including carbon-degrading Singulisphaera under TF20 and nitrifying Nitrosomonadaceae under TF100, and these taxa were correlated with plant and microbial stoichiometry, linking microbial functional groups to nutrient cycling and yield. A moderate (20%) substitution rate therefore best reconciles yield maintenance with nutrient use efficiency, and the effects of organic fertilizer substitution on plant–soil–microbial stoichiometry and provides support for optimizing fertilization strategies.