We demonstrate that a conditional wavefunction theory enables a unified and efficient treatment of the equilibrium structure and nonadiabatic dynamics of correlated electron-ion systems. The conditional decomposition of the many-body wavefunction formally recasts the full interacting wavefunction of a closed system as a set of lower dimensional (conditional) coupled `slices. We formulate a variational wavefunction ansatz based on a set of conditional wavefunction slices, and demonstrate its accuracy by determining the structural and time-dependent response properties of the hydrogen molecule. We then extend this approach to include time-dependent conditional wavefunctions, and address paradigmatic nonequilibrium processes including strong-field molecular ionization, laser driven proton transfer, and Berry phase effects induced by a conical intersection. This work paves the road for the application of conditional wavefunction theory in equilibrium and out of equilibrium ab-initio molecular simulations of finite and extended systems.