Soil organic carbon (SOC) is one of the significant soil components influencing soil functions and soil processes. However, little is known about the impact of land-use change on SOC dynamics on coastal agroecosystems. We, therefore, simulated the impact of land use on SOC stock using RothC model under different climate change scenarios. In the present study, natural forest and pasture lands are the native land uses, while cashew, arecanut, and coconut plantations were established about 70–80 years ago from the natural forest. Measured SOC stocks were significantly higher in cashew and forest land uses (109.5 and 88.6 t C/ha) and much lower in coconut, arecanut and pasture lands (64.1–71.0 t C/ha). The study showed that under projected climate change conditions in Goa state and depending on emission scenarios, both decreases and increases of SOC stocks would be possible. By the end of the century, SOC stock in cashew would decrease by 4.3 t C/ha (RCP 4.5) and increase by 2.4 t C/ha (RCP 8.5), in coconut the SOC change was negligible (0.2 t C/ha) in RCP 4.5 while increased by 3.2 t C/ha in RCP 8.5. Arecanut, pasture and forest land uses showed a marked SOC decrease in RCP 4.5 (ranging from 5.2 to 5.4 t C/ha) and negligible positive (0.6–0.7 t C/ha) or negative (0.6 t C/ha) changes in RCP 8.5. Overall, the model indicated cashew plantations as the most prominent sink of SOC storage, while coconut and pasture are not viable sinks of SOC in the study area. We suggest promoting cashew, arecanut, and coconut land use system integrated with tree components and pasture to improve the SOC storage and other ecosystem services in the coastal agroecosystem.