An energetically balanced, implicit integrator for non-hydrostatic vertical atmospheric dynamics on the sphere is presented. The integrator allows for the exact balance of energy exchanges in space and time for vertical atmospheric motions by preserving the skew-symmetry of the non-canonical Hamiltonian formulation of the compressible Euler equations. Essential to the efficient implementation of such an integrator is a preconditioning strategy that reduces the dimensionality of the inner linear system. Here we reduce the four component velocity, density, density weighted potential temperature and Exner pressure system into a single equation for the density weighted potential temperature via repeated Schur complement decomposition and the careful selection of coupling terms. The integrator is validated for standard test cases of baroclinic stability and a non-hydrostatic gravity wave on the sphere, and shows robust convergence in both regimes.