Managing croplands for increased storage of soil organic matter (SOM) contributes to the development of resilient farming systems in a changing climate. We examined SOM dynamics in a wheat (Triticum durum L.) – maize (Zea mays L.) irrigated bed planting system established near Ciudad Obregón, Sonora, Mexico. Soil samples (0–15 cm) were collected from conventionally tilled raised beds (CTB) with all crop residues incorporated (CTB-I) and permanent raised beds (PB) with crop residues burned (PB-B), removed (PB-R), partly retained (PB-P) or fully retained (PB-K) receiving 0, 150 or 300 kg N ha−1, and analyzed for organic C (OC), total N (TN) and δ13C in whole-soil, light fraction (LF) and coarse- (sand) and fine- (silt and clay) mineral-associated organic matter (MAOM). Results indicated that PB-K and PB-B increased soil OC (p <0.05) in whole-soil relative to CTB-I, mainly through increases in sand- and silt-size MAOM, respectively. Similarly, N-fertilization increased soil OC and TN contents in whole-soil, coarse-MAOM and fine-MAOM, but not in the LF pool. Soil δ13C was higher (p <0.05) in PB-K (−20.18‰) relative to PB-B (−20.67‰), possibly due to the stabilization of partly decomposed maize-C in silt- and clay-size MAOM. Composition of SOM surveyed by CPMAS 13C NMR was not affected by tillage-residue management, and roughly consisted of 35% O-alkyl-C, 31% alkyl-C, 24% aromatic-C and 10% carboxyl-C. Our results indicate that long-term PB-K and PB-B adoption increased surface soil OC contents relative to CTB-I, even though pathways of SOM stabilization differed between systems. Under PB-K, accumulation of fine-MAOM was mostly related to straw-C inputs, whereas in PB-B it was closely associated to black-C precursors. Fine-MAOM appeared responsive to crop residue management, and should be therefore considered when analyzing mechanisms of SOM stabilization in irrigated croplands.