Silicon quantum dots (SiQDs) were synthesized from N-[3-(trimethoxysilyl)propyl]-ethylenediamine and catechol by a hydrothermal method. Transmission electron microscopy, Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy were used to characterize the morphology and structure of quantum dots. The SiQDs were then placed on gold nanoparticles (AuNPs). When Cys is added to this solution, Cys will penetrate the SiQDs "shell" of the SiQDs/AuNP composite. This is due to the interaction and conformational differences of Cys and other substance with AuNPs and leads to the dispersion of the aggregated SiQD/AuNPs. A color change from purple to red can be visually observed, and the (green) fluorescence of SiQDs (with excitation/emission peaks at 430/520 nm) is restored. This dual-readout nanoprobe was successfully applied to the selective and sensitive detection of cysteine (Cys) in (spiked) serum and urine samples. The detection limit is 3.5 nmol·L (at an S/N ratio of 3), and the method works on the 0.01 to 2 μM Cys concentration range. Graphical abstract Schematic illustration of a method for synthesizing silicon quantum dots (SiQDs) and coating them on gold nanoparticles (AuNPs) as an optical probe for colorimetric and fluorometric determination of cysteine.