Ca2+ acts as an important cellular second messenger in eukaryotes. In both plants and animals, a wide variety of environmental and developmental stimuli trigger Ca2+ transients of a specific signature that can modulate gene expression and metabolism. In animals, mitochondrial energy metabolism has long been considered a hotspot of Ca2+ regulation, with a range of pathophysiology linked to altered Ca2+ control. Recently, several molecular players involved in mitochondrial Ca2+ signalling have been identified, including those of the mitochondrial Ca2+ uniporter. Despite strong evidence for sophisticated Ca2+ regulation in plant mitochondria, the picture has remained much less clear. This is currently changing aided by live imaging and genetic approaches which allow dissection of subcellular Ca2+ dynamics and identification of the proteins involved. We provide an update on our current understanding in the regulation of mitochondrial Ca2+ and signalling by comparing work in plants and animals. The significance of mitochondrial Ca2+ control is discussed in the light of the specific metabolic and energetic needs of plant and animal cells.