Long-term organic and mineral fertilization can bring in changes in the different pools of soil carbon (C) and nitrogen (N), and sequestration under irrigated soybean-wheat cropping system (SW). Results showed that long-term mineral and organic fertilization (NPK + FYM) significantly (P < 0.05) increased soil reaction (5.96, 6.41 and 6.56) as compared to unfertilized control (CK), however, it was 0.24, 0.11 and 0.12 units lower than FYM in all three soil depths. NPK + FYM fertilization clearly indicated that -54, 51 and 52% higher total organic carbon (TOC) and -46, 56 and 55% higher total nitrogen (TN) as compared to CK in 0-15 cm, 15-30 cm and 30-45 cm soil depths, respectively. Average values for TOC and TN with different treated plots were 9.89, 9.23 and 8.57 g kg(-1) and 0.80, 0.74 and 0.68 g kg(-1) under all three soil depths. We conclude that, significantly higher C (-22, 20 and 19 Mg C ha(-1)) and N (1.79, 1.67 and 1.53 Mg N ha(-1)) storage was recorded with NPK + FYM as compared to CK in 0-15 cm, 15-30 cm and 30-45 cm soil depths, respectively. Nevertheless, higher total C and N sequestration rate in 0-45 cm soil depth was noted under NPK + FYM (-1153 and 91 kg ha(-1) year(-1)) treated plot, followed by N + FYM (-981 and 78 kg ha(-1) year(-1)) and FYM alone (-873 and 63 kg C ha(-1) year(-1)). These results clearly indicated that combined organic and mineral fertilization have its positive effect on soil C and N pools, and sequestration in the long-run, and thus, help in maintaining long-term soil sustainability.