Background and Aims: This 11-year study in Alborz province, Iran, explored the effects of organic and inorganic fertilizers on soil organic carbon (SOC), microbial activity, and crop yield in a wheat-maize rotation under semi-arid conditions. The aim was to enhance soil fertility and health through sustainable fertilizer management. Methods: Six treatments were evaluated: control (no fertilizer), standard urea (SU), double urea (DU), standard vermicompost (SV), double vermicompost (DV), and combined urea-vermicompost (HSU+HSV). Soil properties, microbial communities, and crop performance were assessed. Results: Vermicompost treatments (SV, DV, HSU+HSV) significantly increased SOC by 35.4% and reduced soil bulk density by 7.9% compared to urea treatments. DV yielded the highest crop yield (5517 kg ha(-)(1)), 44.7% above control, with enhanced nitrogen use efficiency (22.8 kg grain kg(-)(1) N). Vermicompost boosted Gram-positive bacteria and arbuscular mycorrhizal fungi, while urea increased fungal biomass but reduced microbial diversity. Conclusion: Long-term vermicompost application improved soil quality by enhancing SOC stocks, microbial activity, and nutrient availability, leading to superior crop yields. Combined urea-vermicompost use optimized soil functions and plant performance, offering a sustainable strategy for soil health in wheat-maize rotations under semi-arid conditions.