Biobased residues derived from organic urban waste materials can be processed to produce soil amendments that enhance soil fertility and carbon sequestration. However, the extent of carbon sequestration by biobased residues depends on the interaction between their physicochemical properties, climate, and agroecosystem management practices. Our objective was to predict how different biobased residues (compost, anaerobic digestate, or biosolids), compared to nitrogen fertilizer, affect soil organic carbon stocks under continuous cropping and crop rotation in Ontario, Canada, using the Century model. The Century model was calibrated and validated with data, from a three-year field study located in Elora, Ontario, Canada, that was used to predict long-term changes in soil organic carbon. Our results showed that after 150 years, soil amended with compost and biosolids increased soil organic carbon stocks significantly ( p < 0.05) compared to anaerobic digestate and nitrogen fertilizer. Soil organic carbon stocks were 1%–27% greater with crop rotation compared to continuous cropping. Model performance indicated a strong correlation between measured and simulated soil organic carbon stocks ( R2 = 0.26–0.82; RMSD = 432–727 g m−2). Our findings suggested that compost had the greatest soil carbon sequestration potential of the tested soil amendments, and this difference was due to the quantity and quality of carbon input.