Soil respiration is a crucial source of carbon dioxide (CO2) in the atmosphere. The underlying processes involved are multifaceted, sequential chemical reactions associated with the conversion of soil organic carbon to CO2. In this paper, we present a mechanistic, biogeochemical model to simulate soil CO2 emissions considering the microbial and sequential chemical processes using the well-established hydrological model, Soil and Water Assessment Tool (SWAT) for the first time. The soil CO2 emissions from multiple sequential soil chemical reactions were compared with the observed data at three sites in Canada. The results show that the modelled CO2 emission rates are in good agreement with the observed data with performance statistics: PBIAS: 0.13%-23%; NSE: 0.27 to 0.62; RSR: 0.60 to 0.84; R-2: 0.29 to 0.83. This approach could be used in future regional to global-scale models for simulating the soil CO2 emission and hydrological processes.