Tailoring of the biodegradation of photoluminescent silicon quantum dots (Si QDs) is important for their future applications in diagnostics and therapy. Here, the effect of drying and surface pretreatment on the dissolution rate of Si QDs in model liquids and living cells was studied in vitro using a combination of photoluminescence and Raman micro-spectroscopy. Porous silicon particles were obtained by mechanical milling of electrochemically etched mesoporous silicon films, and consist of interlinked silicon nanocrystals (QDs) and pores. The samples were subjected to super-critical drying with CO2 solvent (SCD) or air drying (AD) and then annealed at 600 °C for 16 hours in 1% oxygen to obtain nano-sized Si QDs. The obtained samples were characterized by a core-shell structure with a crystalline silicon core and a SiO2 layer on the surface. The sizes of the crystalline silicon cores, calculated from Raman scattering spectra, were about 4.5 nm for the initial AD-SiQDs, and about 2 nm for the initial SCD-SiQDs. Both the AD-Si QDs and the SCD-Si QDs exhibited visible photoluminescence (PL) properties due to quantum confinement effects. The dissolution of the nanocrystals was evaluated through their PL quenching, as well as by the presence of a low-frequency shift, broadening, and a decrease in the intensity of the Raman signal. The stability of the AD-Si QDs and the complete dissolution of the SCD-Si QDs during 24 hours of incubation with cells have been demonstrated. This might explain the apparent lower cytotoxicity observed for SCD-Si QDs.