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 Nc 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 Nc, 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.