A novel approach for nanofabricating protein-functionalized luminescent silicon nanoparticles based on infrared ultrafast laser ablation of silicon in an aqueous solution of Staphylococcus aureus protein A is reported. It is demonstrated that 8 nm protein A-capped silicon quantum dots with blue-green photoemissive properties are generated. The conjugation efficiency studies reveal a high percentage of protein A attached to the Si nanoparticle surface through physical adsorption phenomena during the in situ laser process. The biological functionality of laser-generated Staphylococcus aureus protein A-capped Si nanoparticles is investigated. Confocal and electron microscopy together with energy dispersive x-ray spectroscopy analysis show that these Si-based bio-nanostructures selectively bind IgG in the cells. Cell viability studies reveal that these protein A-capped Si nanoparticles are suitable for biological applications, demonstrating their potential as universal secondary biomarkers for in vivo applications such as long-term, real-time cell labeling, cell staining and controlled drug delivery.