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Abstract Incorporating protection against quantum errors into adiabatic quantum computing (AQC) is an important task due to the inevitable presence of decoherence. Here, we investigate an error-protected encoding of the AQC Hamiltonian, where qubit ensembles are used in place of qubits. Our Hamiltonian only involves total spin operators of the ensembles, offering a simpler route towards error-corrected quantum computing. Our scheme is particularly suited to neutral atomic gases where it is possible to realize large ensemble sizes and produce ensemble-ensemble entanglement. We identify a critical ensemble size N c where the nature of the first excited state becomes a single particle perturbation of the ground state, and the gap energy is predictable by mean-field theory. For ensemble sizes larger than N c, the ground state becomes protected due to the presence of logically equivalent states and the AQC performance improves with N, as long as the decoherence rate is sufficiently low.