Soil carbon dynamics and sequestration potential are indicators of both climate change mitigation and soil health restoration. Carbon source-sink relationships in rice-based cropping systems strongly influence nutrient availability and greenhouse gas (GHG) balance. A field experiment was conducted at Integrated Farming System Research Station, Karamana, Kerala Agricultural University, to assess carbon dynamics under 8 different rice-based cropping sequences designed for soil health improvement, family nutrition, livestock feed supply and income generation. The conventional rice-fallow-fallow system served as the control. Soil samples collected at 3 depths (0–15, 15–30 and 30–45 cm) after seasonal crop residue incorporation were analysed for total organic carbon (TOC), carbon pools (labile and non-labile), particulate organic carbon (POC), water-soluble carbon (WSC) and microbial biomass carbon (MBC). Carbon fractions consistently declined with depth (0–15 cm > 15–30 cm > 30–45 cm), reflecting reduced organic inputs and microbial activity. Among the sequences, the soil health-oriented system T3 (rice-bush cowpea-groundnut + daincha) recorded the highest TOC (6.27 %), organic carbon (1.38 %) and MBC (326.48 mg kg-1), while T4 (rice + daincha-rice + daincha-redgram + groundnut) achieved highest WSC (84.52 mg kg-1) and POC (4.11 %). The income-oriented system T9 (rice-sweet potato-cucumber) ranked second for most carbon pools and attained the highest carbon management index (290.48). Notably, T9 also achieved a net negative GHG balance (-11920 kg CO₂ equivalent), underscoring the role of bioresource incorporation in enhancing soil carbon sequestration, improving soil health and strengthening climate resilience.