The long-term recovery of the oceans from present and past acidification is possible due to neutralization by the dissolution of biogenic CaCO3 in bottom sediments, that is, carbonate compensation. However, such chemical compensation is unable to account for all features of past acidification events, such as the enhanced accumulation of CaCO3 at deeper depths after acidification. This overdeepening of CaCO3 accumulation led to the idea that an increased supply of alkalinity to the oceans, via amplified weathering of continental rocks, must accompany chemical compensation. Here we discuss an alternative: that changes to calcification, a biological process dependent on environmental conditions, can enhance and modify chemical compensation and account for overdeepening. Using a simplified ocean box model with both constant and variable calcification, we show that even modest drops in calcification can lead to appreciable long-term alkalinity build-up in the oceans and, thus, create overdeepening; we term this latter effect biological compensation. The chemical and biological manifestations of compensation differ in terms of controls, timing and effects, which we illustrate with model results. To better predict oceanic evolution during the Anthropocene and improve the interpretation of the palaeoceanographic record, it is necessary to better understand biological compensation.