Secretory Pathway Ca²⁺/Mn²⁺ ATPases (SPCAs) are important for maintenance of cellular Ca²⁺ and Mn²⁺ homeostasis and to date, all SPCAs have been found to localise to the Golgi apparatus. The single Drosophila SPCA (SPoCk) gene was identified by an in silico screen for novel Ca²⁺ ATPases. It encodes three SPoCk isoforms with novel, distinct sub-cellular specificities, in the ER and peroxisomes, in addition to the Golgi. Furthermore, expression of the peroxisome-associated SPoCk isoform is sexually dimorphic. Over-expression of organelle-specific SPoCk isoforms impacts on cytosolic Ca²⁺ handling, both in cultured Drosophila cells and in a transporting epithelium, the Drosophila Malpighian (renal) tubule. Specifically, the ER isoform impacts on IP₃-mediated Ca²⁺ signalling; the Golgi isoform impacts on diuresis; whereas the peroxisome isoform co-localises with calcium 'spherites' and impacts on calcium storage and transport. RNAi directed against the common exons of the three SPoCk isoforms results in aberrant Ca²⁺ signaling and abolishes neuropeptide-stimulated diuresis by the tubule. SPoCk thus contributes to both of the contrasting requirements for calcium in transporting epithelia: to transport or store calcium in bulk, without compromising its use as a signal.