Soil organic carbon (SOC) is a major indicator of soil quality and/or health but its slow short-term response to management changes has prompted the search for more sensitive indicators for monitoring short-term changes in soil organic matter (SOM). This study aimed to investigate the short-term effects of crop rotation systems and residue management practices under no tillage on selected soil carbon fractions of a Haplic Cambisol, using plots from a conservation agriculture (CA) field trial (split plot design replicated in three blocks). The main plots were comprised of the crop rotation systems: maize-fallow-maize (MFM), maize-fallow-soybean (MFS), maize-wheat-maize (MWM) and maize-wheat-soybean (MWS). Residue management practices that included residue removal (R−) and residue retention (R+) were allocated to the sub-plots. The carbon fractions measured were SOC, microbial biomass carbon (MBC), mineralisable carbon (Cmin) and particulate organic matter carbon fractions (POM-C). Crop rotation systems significantly (p < 0.05) influenced Cmin and POM-C fractions whereas residue management practices significantly (p < 0.05) affected all the carbon fractions. Crop residue retention as opposed to its removal enhanced all the carbon pools. The POM-C and Cmin fractions were more sensitive to short-term CA management interventions than SOC and MBC, therefore they can be used for monitoring SOM changes and microbial activities.