Purpose <p>Considering the pressing concerns regarding food security amid climate change, it is imperative to adopt sustainable agricultural practices that enhance soil organic carbon (SOC) sequestration and crop productivity. Therefore, the objective of this study was to investigate the changes in SOC pools, microbial metabolic quotient (<i>q</i>CO₂), and extracellular enzymes activities under long-term cropping systems.</p> Materials and methods <p>A long-term field experiment (≥ 12 years) consisted of rice-wheat (W-R), maize-wheat (W-M), and legume-wheat (W-L) was established as randomized complete block design with three replications. The W-R system was used as reference, as it represents the most traditional cereal based rotation in the region.</p> Results and discussion <p>After 12 years of experimentation, SOC increased by 20% in W-M and 43% in W-L compared to W-R (5.42&#xa0;g kg⁻¹). Nitrogen (N), phosphorus (P), and potassium (K) availability was significantly enhanced under diversified systems (W-L &gt; W-M &gt; W-R). Soil microbial biomass carbon (SMBC) and nitrogen (SMBN) increased by up to 43%, while cellobiohydrolase and β-glucosidase activities increased by 90% in the W-L and W-M systems compared to the W-R system. Similarly, SOC mineralization was 12–31% higher in W-L and W-M, and positively correlated with elevated labile SOC fractions. Recalcitrant carbon was unaffected by cropping systems. Notably, W-L reduced the <i>q</i>CO₂ by 19%, indicating a likely higher microbial carbon use efficiency.</p> Conclusions <p>These findings demonstrate that diversified cropping systems, particularly those including legumes (W-L), increase SOC labile pools by improving <i>q</i>CO₂ and stabilizing carbon pools, thereby offering a viable strategy for carbon sequestration and climate change mitigation, improving soil quality, and supporting global food security.</p>