Crop residue management in cereal-cereal based cropping systems poses formidable challenge globally. This study aimed to investigate the long-term effects of residue management practices (RMPs) like crop residue incorporation (CRI), biochar (BC) produced from crop residue, crop residue burning (CRB), and complete residue removal (CRR) on soil aggregation and carbon (C) accumulation under major cereal-based systems, viz. wheat-maize/pearl millet/rice cropping systems (WMCS/WPCS/WRCS). The study was part of a long-term field experiment started in 2009 used a split-plot design with three cropping systems, viz. WMCS, WPCS, and WRCS as main plots and different RMPs as subplots. Soil samples (0-15, 15-30, and 30-60 cm) were analysed for aggregate distribution/stability, and biochemical parameters viz., glomalin, carbohydrates, polysaccharides, and total organic carbon (TOC) within aggregates. The canonical discriminant analysis (CDA) was done to determine the most sensitive variable deciding the aggregate stability and C accumulation. Significant (P < 0.05) effects of cropping systems and RMPs on macroaggregate distribution and biochemical parameters up to 30 cm depth were recorded. WMCS notably increased macroaggregates in upper soil layers. Biochar application proved most effective, enhancing soil aggregation and stability across depths. In 0-15 cm depth, BC-treated plots showed the highest geometric mean diameter (GMD), surpassing CRI, CRB, and CRR by 2.77%, 8.82%, and 10.40%, respectively. Biochar-amended WMCS exhibited enhanced aggregation due to greater TOC accumulation within aggregates. The study highlights the advantages of BC application and CRI under WMCS, WPCS compared to WRCS in improving overall soil health and C-sequestration, while also emphasizing the detrimental effects of CRB and CRR.