Being the second most abundant element on earth after oxygen, silicon remains the working horse for key technologies for the years. Novel photonics platform for high-speed data transfer and optical memory demands higher flexibility of the silicon modification, including on-chip and in-bulk inscription regimes. These are deepness, three-dimensionality, controllability of sizes and morphology of created modifications. Mid-IR (beyond 4 µm) ultrafast lasers provide the required control for all these parameters not only on the surface (as in the case of the lithographic techniques), but also inside the bulk of the semiconductor, paving the way to an unprecedented variety of properties that can be encoded via such an excitation. We estimated the deposited energy density as 6 kJ cm−3 inside silicon under tight focusing of mid-IR femtosecond laser radiation, which exceeds the threshold value determined by the specific heat of fusion (~ 4 kJ cm−3). In such a regime, we successfully performed single-pulse silicon microstructuring. Using third-harmonic and near-IR microscopy, and molecular dynamics, we demonstrated that there is a low-density region in the center of a micromodification, surrounded by a “ring” with higher density, that could be an evidence of its micro-void structure. The formation of created micromodification could be controlled in situ using third-harmonic generation microscopy. The numerical simulation indicates that single-shot damage becomes possible due to electrons heating in the conduction band up to 8 eV (mean thermal energy) and the subsequent generation of microplasma with an overcritical density of 8.5 × 1021 cm−3. These results promise to be the foundation of a new approach of deep three-dimensional single-shot bulk micromachining of silicon.