In this work, scanning microwave microscopy (SMM) is used to monitor the evolution of the local microwave response, in terms of variations in the S11 input reflection coefficient, in two III–V heterostructures relevant to mid-infrared photonics, namely a 150 nm thick heavily doped InGaAs layer on InP and HfO2 (35 nm)/InGaAs (150 nm)/InP, subjected to Ga+ FIB milling over a broad dose range. By correlating raw, uncalibrated two-dimensional S11 maps with atomic force microscopy (AFM) and Raman spectroscopy, we observe a dose-dependent evolution from implantation-dominated behavior to progressive amorphization, layer thinning and surface roughening. In the uncapped InGaAs/InP system, the SMM response varies monotonically with ion dose, consistent with progressive FIB-induced modification of the exposed InGaAs layer and, at larger milling depths, of the underlying InP substrate. In the HfO2-capped structure, the microwave response is more complex: the oxide initially acts as a partial buffer against ion penetration, delaying damage transfer, but this effect progressively weakens as the cap is thinned and structurally degraded. The resulting S11 contrast may reflect the combined effects of FIB-induced structural modifications, layer removal, local material composition, and surface morphology. Overall, the combined dataset indicates that SMM is a potentially highly sensitive probe of FIB-induced nanoscale modifications in the local microwave response, especially at low doses, provided that suitable on-chip calibration and de-embedding structures are available.