The phase separation of a two-dimensional active binary mixture is studied under the action of an applied shear through numerical simulations. It is highlighted how the strength of the external flow modifies the initial shape of growing domains. The activity is responsible for the formation of isolated droplets which affect both the coarsening dynamics and the morphology of the system. The characteristic dimensions of domains along the flow and the shear direction are modulated in time by oscillations whose amplitudes are reduced when the activity increases. This induces a broadening of the distribution functions of domain lengths with respect to the passive case due to the presence of dispersed droplets of different sizes.