This study presents the spatial variability and dynamics of soil organic carbon (SOC), soil organic matter (SOM) and soil pH contents at the Wonji Shoa Sugar Estate (WSSE), Ethiopia. Soil samples were collected immediately after the sugarcane was harvested and then analysed for SOC, SOM and pH content using standard procedures. The analysis results showed that the pH value varied between 6.7–8.4 (neutral to moderately alkaline) and 7.3–8.5 (neutral to strongly alkaline) for the top and bottom soil profiles, respectively. The SOM content is in the range of 1.1–6.7% and 0.74–3.3% for the upper and lower soil layers, respectively. Nearly 45% of the samples demonstrated a SOM content below the desirable threshold (<2.1%) in the bottom layer and, hence, inadequate. Moreover, most of the topsoil layer (95%) has an SOM content exceeding the desirable limit and hence is categorized within the normal range. Interestingly, the SOC content showed a spatial variability in both the surface and sub-surface soil layers. A lower SOC and SOM content was found for the sub-soil in the south and southwestern part of the plantation. A further decline in the SOC and SOM content may face the estate if the current waterlogging condition continues in the future for a long period. Overall, the study result emphasizes the need to minimize the pre-harvest burning of sugarcane and action is needed to change the irrigation method to green harvesting to facilitate the SOC retention in the soil and minimize the greenhouse emission effect on the environment, hence improving soil quality in the long-term.