With an increasing interest in closing the nutrient loop in agroecosystems, organic amendments are highly recommended as a reliable resource for soil nutrient recycling. However, from a carbon sequestration perspective, not much has been reported on the contribution of different organic amendments to soil organic carbon (SOC), crop carbon (C) uptake, and soil carbon dioxide (CO2) emissions in wheat-maize cropping systems of sloppy upland soil. To fill the knowledge gap, a two-year lysimeter-field plots experiment was conducted in a sloppy upland purplish soil under wheat-maize cropping systems. The experiments were arranged in a complete random block design with five treatment plots, namely; fresh pig slurry as organic manure (OM), crop residues (CR), conventional mineral fertilizers (NPK) as the control, organic manure plus mineral fertilizers (OMNPK), and crop residues plus mineral fertilizers (CRNPK). Our results showed the leaf photosynthesis rate was not significantly increased by organic amendment application treatments compared to NPK treatment, and was within a range of 4.8 to 45.3 µmol m−2 s−1 for the wheat season and −20.1 to 40.4 µmol m−2 s−1 for the maize season across the five treatments and the measured growth stages. The soil CO2 emissions for the maize season (in the range of 203 to 362 g C m−2) were higher than for the wheat season (in the range of 118 to 252 g C m−2) on average across the different experimental treatments over the two-year experiment. The organic amendment application increased annual cumulative CO2 emissions from 30% to 51% compared to NPK treatment. Over the two years, the average crop C uptake ranged from 174 to 378 g C m−2 and from 287 to 488 g C m−2 for the wheat and maize seasons, respectively, and the organic amendment application increased the crop C uptake by 4% to 23% compared to NPK treatment. In the organic amendment treatments, the C balance ranged from −160 to 460 g C m−2 and from −301 to 334 g C m−2 for the wheat and the maize seasons, respectively, which were greater than those in the NPK treatment. Overall, the present study results suggest incorporation of organic amendments could be an effective strategy for increasing C sequestration and sustaining crop productivity in sloppy upland soil.