Soil conservation and carbon sequestration are critical issues in the Indian Himalayas. This study, conducted from 2005 through 2009 on a sandy clay loam soil near Almora, India, with two tillage (conventional tillage [CT] and zero tillage [ZT]) and five fertilization management practices (100% NPK [F1], 50% NPK + 10 Mg farmyard manure [FYM] ha⁻¹ [F2], 50% NPK + 10 Mg poultry manure [PM] ha⁻¹ applied on equivalent N basis of 10 Mg FYM ha⁻¹ [F3], 100% NPK + 10 Mg FYM ha⁻¹ [F4], and 100% NPK + 10 Mg PM ha⁻¹ applied on equivalent N basis of 10 Mg FYM ha⁻¹ [F5]). The effects of these practices on soil organic carbon (SOC) retention and its physical and chemical pools, soil aggregation, and aggregate-associated C contents in the 0- to 15-cm soil layer were evaluated. The plots under ZT had nearly 11% and 12% higher total SOC and particulate organic matter–C (POM-C) concentrations, respectively, compared with CT (∼12 and 4 g kg⁻¹ soil, in that order) plots in the 0- to 5-cm soil layer. Plots under F4 and F5 had significantly higher total SOC and POM-C contents than F2- and F3-treated plots in both soil layers. Although the labile pools of SOC were positively affected by ZT and fertilization, the recalcitrant pool was not. Plots under ZT had higher macroaggregates, mean weight diameter (MWD), and macroaggregate-associated SOC compared with CT in the surface soil layer only. Similarly, F4- or F5-treated plots had higher macroaggregates, MWD, and macroaggregate-associated SOC compared with F1-, F2-, or F3-treated plots in that layer. All C pools had significant positive relationship with the MWD (in millimeters) in the 0- to 5-cm soil layer (n = 40), except for the nonlabile pool. However, only very labile (Pool I) and labile (Pool II) C pools had significant relationships with the proportion of macroaggregates in the 0- to 5-cm soil layer. Thus, adoption of year-round ZT along with 100% NPK in rice and 100% NPK + FYM/PM addition in wheat is the best management option under an irrigated rice-wheat system in the Indian Himalayas, as the management practice has the potential to maintain productivity and improve soil aggregation with greater accumulation of POM-C and SOC stabilization.