Nuclear quantum phenomena beyond the Born–Oppenheimer approximation are known to play an important role in a growing number of chemical and biological processes. While there exists no unique consensus on a rigorous and efficient implementation of coupled electron–nuclear quantum dynamics, it is recognized that these problems scale exponentially with system size on classical processors and, therefore, may benefit from quantum computing implementations. Here, we introduce a methodology for the efficient quantum treatment of the electron–nuclear problem on near-term quantum computers, based upon the Nuclear–Electronic Orbital (NEO) approach. We generalize the electronic two-qubit tapering scheme to include nuclei by exploiting symmetries inherent in the NEO framework, thereby reducing the Hamiltonian dimension, number of qubits, gates, and measurements needed for calculations. We also develop parameter transfer and initialization techniques, which improve convergence behavior relative to conventional initialization. These techniques are applied to H2 and malonaldehyde for which results agree with NEO full configuration interaction and NEO complete active space configuration interaction benchmarks for ground state energy to within 10−6 hartree and entanglement entropy to within 10−4. These implementations therefore significantly reduce resource requirements for full quantum simulations of molecules on near-term quantum devices while maintaining high accuracy.