The investigation of surface-induced lattice-strain effects in free-standing silicon nanocrystals (Si NCs) is fundamental in view of the materialization of nanosilicon-based technologies that exploit the unique properties of silicon at the nanoscale. In this work, a comprehensive investigation in free-standing Si NCs is performed, aimed at unveiling physical phenomena related to surface oxidation upon exposure to air, from which strongly surface-dependent lattice strain is found. Raman and infrared spectroscopy techniques are used to monitor the time evolution of the oxidation, through which a clear correlation between the formation of a superficial native oxide and the appearance of compressive strain in the nanocrystals' core is found, which increases continuously as the oxidation progresses. By comparing experimental data with simulations using an improved phonon confinement model, it is concluded that strain is negligible in H-terminated nanocrystals with sizes of approximately 3 nm. After long-term natural oxidation, the compressive stress imposed by the native oxide shell is estimated to be 1.2 GPa. The results presented here link the time-dependent oxidation phenomenon with the experimental observation of compressive strain in free-standing Si NCs, clarifying contradicting results found in the literature, and demonstrate a simple route for the deconvolution of confinement and strain effects in low-dimensional structures using Raman spectroscopy.