Stimulation of receptors on the surface of animal cells often evokes cellular responses by raising intracellular Ca2+ concentration [1]. The rise in cytoplasmic Ca2+ drives a plethora of processes, including neurotransmitter release, muscle contraction, and cell growth and proliferation [2]. Mitochondria help shape intracellular Ca2+ signals through their ability to rapidly take up significant amounts of Ca2+ from the cytosol via the uniporter [3-10], a Ca2+-selective ion channel in the inner mitochondrial membrane [11]. The uniporter is subject to inactivation [12-14], whereby a sustained cytoplasmic Ca2+ rise prevents further Ca2+ uptake [15]. In spite of its importance in intracellular Ca2+ signaling, little is known about the mechanism underlying uniporter inactivation. Here, we report that maneuvers that promote matrix alkalinisation significantly reduce inactivation whereas acidification exacerbates it. We further show that the F1F0-ATP synthase complex is an important source of protons for inactivation of the uniporter. These findings identify a novel molecular mechanism that regulates the activity of this ubiquitous intracellular Ca2+ channel, with implications for intracellular Ca2+ signaling and aerobic ATP production.