The zincophosphate [Zn₃(PO₄)₂(HPO₄)]·H₃N(CH₂)₆NH₃·H₃BO₃, I, has been synthesized by mild hydrothermal methods, and the crystal structure determined by single-crystal X-ray diffraction. In the structure, corner-linked ZnO₄, PO₄ and PO₃(OH) tetrahedra form anionic layers that contain 3-, 4-, 5- and 8-membered rings and may be considered constructed from columns of Zn₅P₄ cage-like building units. The layers are interleaved by composite layers of diprotonated 1,6-diaminohexane and boric acid molecules. The acid molecules stabilize a bilayer-like arrangement of the organic dications. The templates interact with the zincophosphate layers by N–H⋯O and O–H⋯O hydrogen bonds. According to thermogravimetry, variable-temperature powder X-ray diffraction and FT-IR spectroscopy studies, I transforms at 478 K into another crystalline layered zincophosphate with release of one water molecule per formula unit originating from condensation between terminal P–OH groups and boric acid molecules. The crystallinity disappears at ca. 600 K.