Conservation agriculture (CA) is an effective tool that is used to increase soil C sequestration and enhance soil quality and agronomic productivity. However, rigorous empirical evidence from Southeast Asia, particularly in the Cambodian agro-ecosystem, is still scarce. We hypothesized that high and diversified biomass-C inputs in CA might be the first step toward to increase SOC in the topsoil by creating the C flow to support C storage overtime. Thus, the aim of this study was to quantify the short-term (i.e., five year) impacts of soil management and cropping systems on soil organic C (SOC), soil total N (STN), particulate organic C (POC) and mineral-associated organic C (MAOC). There were three distinct experiments comprised of a combination of cover and main crops including rice-, soybean- and cassava-based cropping systems, hereafter designated as RcCS, SbCS and CsCS, respectively. The experimental plots were laid out in a randomized complete block design with three replicates. Soil management treatments included conventional tillage (CT) and no-till (NT) and a selected adjacent area of reference vegetation (RV). Soil sampling was conducted in 2011 and 2013 at seven depths (0–5, 5–10, 10–20, 20–40, 40–60, 60–80 and 80–100 cm). Soil management and crop sequences significantly affected SOC and STN stocks in all three cropping systems. On average, NT SOC stocks at 0–5 cm depth was greater than those of CT by 10%, 20% and 18% and STN stocks by 8%, 25% and 16% for RcCS, SbCS and CsCS, respectively. SOC levels followed the order RV > NT > CT. SOC stocks in the subsoil layers were consistently lower in NT than in CT in all three cropping systems. POC stocks at 0–5 cm depth in NT were on average 22%, 20% and 78% greater than those in CT in RcCS, SbCS and CsCS, respectively. However, significant differences were detected only in RcCS and CsCS. The major POC stocks were found at 0–20 cm depth. NT treatments in SbCS stored 9% greater MAOC stocks at 0–5 cm depth than thos