The title compound, C6H9BrN2O6P2, a micromolar inhibitor of the farnesyl pyrophosphate synthase, is a Z-isomer zwitterion with one negative phosphonate group and a protonated pyridine N atom. Two types of ribbons, both parallel to the a axis, formed by several centrosymmetrically related O-H...O and N-H...O hydrogen bonds are generated in the crystal structure. The resulting two-dimensional (001) "double-layered" networks are joined into a three-dimensional network via inversion-related halogen-oxygen interactions.