We explore an approach to the coherent control and manipulation of quantum degrees of freedom in disordered, interacting systems in the many-body localized phase. Our approach leverages a number of unique features of many-body localization: a lack of thermalization, a locally gapped spectrum, and slow dephasing. We propose a protocol which enables one to efficiently prepare a many-body system into an effective eigenstate, encode quantum information, perform a universal set of gates, and ultimately readout the resulting state without the full microscopic knowledge of the Hamiltonian of the system. Finally, we provide an estimate for the fidelity of our protocol.