Sustainability concerns have led to a shift in the cement industry from ordinary Portland cement (OPC) to the production of low-clinker cements over the past few decades. Low-clinker cements exhibit lower pore alkalinity and denser microstructure due to the consumption of portlandite during the formation of secondary calcium silicate hydrate (C-S–H). Understanding the effects of alterations in pore structure and pore solution composition on the initiation period of service life requires modeling the involved processes. In this paper, we aim to develop a numerical model that combines semi-empirical models within a framework to facilitate the determination of inputs such as diffusion coefficients and buffer capacity. Relative humidity, carbon dioxide diffusion, and carbonation reactions are integrated into a cohesive unit to predict carbonation depth. Finally, the results obtained using different semi-empirical relations are compared. Furthermore, the service life during the initiation phase for different cover depths and cement type (OPC, Portland Pozzolana Cement (PPC), and Limestone Calcined clay cement (LC3)) were determined from numerical simulation under natural environment and compared.