Climate change impacts on ocean biogeochemistry are expected to alter calcium carbonate formation by organisms, necessitating accurate predictive models based on physiological mechanisms. Dynamic Energy Budget (DEB) theory offers a mechanistic and integrative framework to model the metabolism of organisms under changing environmental conditions. Here, we propose a generalized approach to include effects of ocean acidification in DEB modeling by formulating the impacts of changes in saturation state (SS) on the bioenergetics of calcification. While applicable to any species capable of biogenic calcification (microalgae, shellfish, fish, or corals), the model was tested on five bivalve species for which extensive tissue and shell data were available. The model was successfully applied to larval, juvenile, and adult life stages compared to published data. It reproduced typical tissue and shell growth patterns under favourable SS with more accuracy than a typical DEB model. We explored the effects of more detrimental SS values for biocalcification on shell and tissue dynamics and identified missing data and experiments that should help calibrate model parameters. This work represents a necessary step to predict the physiological response of biocalcifiers to changes in ocean acidification. It may also provide a needed mechanistic tool for shell dynamics to be integrated in nutrient cycling models.