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Deformation of all materials necessitates the collective propagation of various microscopic defects. On Earth, fracturing gives way to crystal-plastic deformation with increasing depth resulting in a “brittle-to-ductile” transition (BDT) region that is key for estimating the integrated strength of tectonic plates, constraining the earthquake cycle, and utilizing deep geothermal resources. Here, we show that the crossing of a BDT in marble during deformation experiments in the laboratory is accompanied by systematic increase in the frequency of acoustic emissions suggesting a profound change in the mean size and propagation velocity of the active defects. We further identify dominant classes of emitted waveforms using unsupervised learning methods and show that their relative activity systematically changes as the rocks cross the brittle–ductile transition. As pressure increases, long-period signals are suppressed and short-period signals become dominant. At higher pressures, signals frequently come in avalanche-like patterns. We propose that these classes of waveforms correlate with individual dominant defect types. Complex mixed-mode events indicate that interactions between the defects are common over the whole pressure range, in agreement with postmortem microstructural observations. Our measurements provide unique, real-time data of microscale dynamics over a broad range of pressures (10 to 200 MPa) and can inform micromechanical models for semi-brittle deformation.