The regulation of calcium (Ca) homeostasis is a critical process in both plant and animal systems, involving complex interplay between various organelles and a diverse network of channels, pumps, and transporters. This review provides a concise overview of inter-organellar Ca homeostasis, highlighting key regulators and mechanisms in plant and animal cells. We discuss the roles of key Ca channels and transporters, including IPRs, RyRs, TPCs, MCUs, TRPMLs, and P2XRs in animals, as well as their plant counterparts. Here, we explore recent innovations in structural biology and advanced microscopic techniques that have enhanced our understanding of these proteins' structure, functions, and regulations. We examine the importance of membrane contact sites in facilitating Ca transfer between organelles and the specific expression patterns of Ca channels and transporters. Furthermore, we address the physiological implications of inter-organellar Ca homeostasis and its relevance in various pathological conditions. For extended comparability, a brief excursus into bacterial intracellular Ca homeostasis is also made. This meta-analysis aims to bridge the gap between plant and animal Ca signaling research, identifying common themes and unique adaptations in these diverse biological systems.