TPC2 is a pathophysiologically relevant lysosomal ion channel that is activated directly by the phosphoinositide PI(3,5)P
2
and indirectly by the calcium ion (Ca
2+
)–mobilizing molecule NAADP through accessory proteins that associate with the channel. TPC2 toggles between PI(3,5)P
2
-induced, sodium ion (Na
+
)–selective and NAADP-induced, Ca
2+
–permeable states in response to these cues. To address the molecular basis of polymodal gating and ion-selectivity switching, we investigated the mechanism by which NAADP and its synthetic functional agonist, TPC2-A1-N, induced Ca
2+
release through TPC2 in human cells. Whereas NAADP required the NAADP-binding proteins JPT2 and LSM12 to evoke endogenous calcium ion signals, TPC2-A1-N did not. Residues in TPC2 that bind to PI(3,5)P
2
were required for channel activation by NAADP but not for activation by TPC2-A1-N. The cryptic voltage-sensing region of TPC2 was required for the actions of TPC2-A1-N and PI(3,5)P
2
but not for those of NAADP. These data mechanistically distinguish natural and synthetic agonist action at TPC2 despite convergent effects on Ca
2+
permeability and delineate a route for pharmacologically correcting impaired NAADP-evoked Ca
2+
signals.