Non-ablative femtosecond laser processing of transparent substrates involves cumulative, multi-timescale dynamics that hinder precise control of induced structural modifications. Here, we demonstrate a feedback-compatible diagnostic based on mid-infrared transmission monitoring using a continuous-wave QCL emitting at 4.46 µm. This approach enables in situ observation of structural dynamics induced by femtosecond laser irradiation at repetition rates up to 250 kHz. The technique shows sensitivity to key transient phenomena, including melting, crack formation, and bubble nucleation in glass substrates, as well as to mechanical instabilities affecting laser processing stability. This offers a robust approach towards improved control and optimization in femtosecond laser micromachining of transparent materials.