Silicon nanoparticles of 1–5 nm size (SiNPs) were synthesized by a bottom-up (BU) approach involving a chemical wet method. The contribution of different emitters to the overall excitation–emission matrix was analyzed on the assumption that pure substances existing in a unique form show an excitation wavelength-invariant emission spectrum. The occurrence of emitters differing in size and aggregation was supported by transmission electron microscopy (TEM), small-angle X-ray scattering (SAXS), time-resolved single photon counting, and time-resolved anisotropy experiments. The effect on photoluminescence (PL) of the particle surface oxidation as a result of aging is studied and compared to that of surface oxidized particles obtained by a top-down (TD) approach following an electrochemical method with HF etching. Surface oxidation to SiOx seems to introduce two different effects on the SiNP PL. An emission originated in surface states associated to SiOx was identified and observed for SiNPs synthesized by both BU and TD approaches. Blue-shifted excitation–emission spectra associated to a silicon core in embedded SiOx nanostructures were also identified. Theoretical studies were carried out to help understand the observed results.