<p>Biomineralization shapes the geology of our planet and is an integral part of the global carbon cycle. Many calcifying organisms generate biomineral precursors within their cells but the mechanisms controlling carbonate chemistry in the calcifying vesicles remain unknown. Using the sea urchin embryo that is a prime model for biomineralization by intracellular amorphous calcium carbonate (ACC) formation this work demonstrated a high proton permeability of the calcifying cells and their vesicles. Intra-vesicular pH and Ca²⁺ recordings demonstrate highly alkaline conditions in ACC forming endocytotic Ca²⁺-rich vesicles, that are enriched during the mineralization process. Using confocal live-cell imaging we observe how vesicles exocytose their Ca²⁺-rich and alkaline contents to the calcification front. We identify the proton channel Otop2l as a master regulator for membrane proton conductance in calcifying cells, using the membrane potential to control pH conditions at the site of mineral precursor formation. Electrophysiological investigations demonstrate that Otop2l is activated by alkaline conditions as well as Mg²⁺ and Ca²⁺ ions. We provide evidence for high intracellular proton conductance as mechanism to generate alkaline pH conditions in the calcification vesicles. This deep mechanistic knowledge can help explain sensitivities of marine calcifiers to rapid changes in seawater pH in past and future marine habitats.</p>