Carbon-nitrogen (C:N) coupling is a critical process governing soil fertility and ecosystem functioning in agricultural systems. This study compares C:N dynamics in intensive (High fertilizer and tillage) and low-input (Organic and reduced tillage) systems across temperate and Mediterranean agricultural soils. Field experiments and laboratory analyses assessed soil organic carbon (SOC), nitrogen pools, microbial biomass, and enzyme activities. Intensive systems exhibited higher mineral nitrogen but lower SOC stability, with C:N ratios of 8–10, while low-input systems showed higher SOC and balanced C:N ratios (10–12). Microbial activity was more resilient in low-input systems under nutrient stress. These findings suggest that low-input systems promote sustainable C:N coupling, enhancing long-term soil health. Management strategies should prioritize organic inputs and reduced tillage to optimize nutrient cycling.