Discrimination of self from non-self through the continuous selection of effector specificity is the backbone of effective immunity. For natural killer (NK) cells this specificity is achieved by unique combinations of variable germ-line receptors that recognize self-MHC antigens. Inhibitory interaction between NK cell receptors and self-ligands is the key determinant in functional potentiation of pre-primed effector responses, a process termed NK cell education.However, the molecular mechanisms connecting homeostatic surface receptor signalling to an NK cell’s intrinsic functional potential have remained a key knowledge gap. We have found that NK cells expressing self-MHC specific inhibitory killer cell immunoglobulin-like receptors (KIR) show a greater accumulation of dense-core secretory granules, converged closer to the centrosome in resting NK cells. Upon activation, interference of signaling from acidic Ca2+stores reduced both target-specific Ca2+-flux, degranulation and cytokine production. Furthermore, inhibition of PI(3,5)P2 synthesis or genetic silencing of the PI(3,5)P2-regulated lysosomal Ca2+-channel TRPML1 in primary NK cells led to an increase in granular load and enhanced functional potential. These results suggest a model where continuous unopposed signaling through activating receptors render NK cells hypofunctional through TRPML1-mediated modulation of acidic Ca2+stores.