Active flow control in microfluidic devices to broaden the range of desired conditions is a significant practical concern. In this study, we experimentally investigate liquid–liquid parallel flow under the dispersed phase flow-rate pulsations in a T-junction microchannel. Sinusoidal flow rate disturbances with variations in amplitude and period were applied to dispersed phases of different viscosities. The study involves flow visualization and velocity field measurements using the micro-PIV technique for both free and excited flow conditions. The analysis of flow pattern maps, velocity fields, velocity gradients, and phase-averaged velocity profiles in a T-junction region and far downstream provided insights into the evolution of disturbances, which is different in low- and high-viscosity liquids. In the less viscous liquid, transverse waves amplify longitudinal ones due to relaxation of the liquid–liquid interface, while in the high-viscosity dispersed phase, longitudinal waves are damped significantly, with the transverse wave amplitude remaining almost constant. As a result, we revealed two distinct mechanisms of disturbance wave propagation and the loss of parallel flow stability, which are both dependent on the Ohnesorge number of the dispersed phase. Destabilization of the parallel flow led to the formation of plugs with a narrow length distribution. Single-mode, double-mode, triple-mode, and multi-mode plug formation regimes were identified. The results of the study can potentially be used to extend the range of segmented flow regimes and generate plugs of a desired length.