The disclosure describes various aspects of optical control of atomic quantum bits (qubits) for phase control operations. More specifically, the disclosure describes methods for coherently controlling quantum phases on atomic qubits mediated by optical control fields, applying to quantum logic gates, and generalized interactions between qubits. Various attributes and settings of optical/qubit interactions (e.g., atomic energy structure, laser beam geometry, polarization, spectrum, phase, background magnetic field) are identified for imprinting and storing phase in qubits. The disclosure further describes how these control attributes are best matched in order to control and stabilize qubit interactions and allow extended phase-stable quantum gate sequences.