Crop residue management strategies must be adapted for improving carbon (C) balance and soil C stock in agroecosystems in sub-Saharan Africa with consideration of the crop residue availability and site-specific soil characteristics. We conducted field experiments to determine the effects of crop residue application method (incorporation/mulching) and quality (maize/cowpea) and N fertilizer application on the soil respiration rate and soil C stock in the surface soil layer (0-15 cm) in maize croplands with contrasting soil textures (clay/sandy) over 2 years from 2012 to 2014 in Tanzania. At the clay site, the incorporation of maize residues showed a 38% increase in CO2 flux compared to mulching, whereas, at the sandy site, mulching showed a 16% increase compared to the incorporation. At the sandy site, mulching practice retained soil moisture content and apparently enhanced the decomposition of the original soil organic C in the surface layer. It is, therefore, suggested that mulching practice may accelerate a long-term depletion of soil C stock at the sandy site. The cowpea residue incorporation led to rapid decomposition because of its high biodegradability at both sites. The N fertilizer application stimulated the decomposition of labile soil organic matter. The soil C stock in the surface layer did not significantly change after the 2-year experiment, irrespective of crop residue treatment and soil type. In conclusion, adequate crop residue management in terms of suppressing CO2 flux during a cropping season depends on soil type, but the long-term effect on soil C stock is unclear.