Cytosolic calcium is a highly dynamic, tightly regulated, and broadly conserved cellular signal. Calcium dynamics have been studied widely in cellular monocultures, yet in vivo most organs comprise heterogeneous populations of stem and differentiated cells. We examined calcium dynamics in each cell type of the adult Drosophila intestine, a self-renewing epithelial organ where multipotent stem cells give rise to mature absorptive enterocytes and secretory enteroendocrine cells. Here we perform live imaging of whole organs ex vivo, and we employ orthogonal expression of red and green calcium sensors to determine whether calcium oscillations between different cell types are coupled. We show that stem cell daughters adopt strikingly distinct patterns of calcium oscillations when they acquire their terminal fates: Enteroendocrine cells exhibit single-cell calcium oscillations, while long-range calcium waves propagate rhythmically across large fields of enterocytes. These multicellular waves do not propagate through progenitor cells (stem cells and undifferentiated enterocyte precursors), whose oscillation frequency is approximately half that of enteroendocrine cells. Organ-scale inhibition of gap junctions eliminates calcium oscillations in all three cell types, even, intriguingly, in progenitor and enteroendocrine cells that are surrounded only by enterocytes. Our findings establish that cells adopt fate-specific modes of calcium dynamics as they terminally differentiate and reveal that the oscillatory dynamics of different cell types in the same epithelium are paced independently.Competing Interest StatementThe authors have declared no competing interest.