Cambodia has faced drastic agrarian changes over the last twenty years with a rapid and massive transformation of the uplands from forest into arable land. Soil quality depletion is one of the main drivers of the resulting decline in crop productivity and increasing production costs in the uplands of Battambang province. The objective of the study was to assess the early effects of conventional plough-based (20¿cm) management (CT) and two conservation agriculture-based (CA) cropping systems (the use of a single—CAS vs. multiple cover crop species—CAM) on a maize monocropping system using three soil organic carbon (SOC) fractions on Mollisols in Battambang province. SOC content, permanganate oxidizable carbon (POXC) and soil CO2 basal respiration through SituResp® were recorded at a depth of 0–10¿cm. Twelve sampling periods were used over the growth period of the cover crops and during the maize cycle. POXC and SituResp® were highly sensitive to management practices with, across the 12 sampling periods, higher values (p¿<¿.05) under CA than CT, with an average increase of 6% and from 20% to 23%, respectively. No difference was observed in SOC content between the practices in our sampling periods. Seasonal variations were observed in both POXC and SituResp®. POXC underwent larger fluctuations following critical weather events than SituResp®. This study showed that POXC and SituResp® were rapidly sensitive to changes in agricultural management practices. POXC and SituResp® are largely influenced by seasonality and could help clarify the impact of weather patterns on soil C dynamics.