Atom interferometers that operate in the spatial domain through continuous measurement of an atomic beam provide benefits in the elimination of sensor dead time and reduced sensitivity to certain noise sources. Further improving its operation, time-domain control of a spatial-domain interferometer can provide necessary methods of error suppression and dynamic range improvement. We model numerically and experimentally demonstrate methods of time-domain control in a 3D-cooled atomic beam interferometer. We demonstrate suppression of magnetic-field-induced phase noise through rapid reversal of the direction of inertial sensitivity at a rate faster than the inverse interrogation time of the interferometer.