The strong visible photoluminescence (PL) of silicon nanocrystals has recently been the focus of considerable research interest. Nanocrystal composites produced by silicon implantation of a fused silica wafer followed by high-temperature thermal processing are characterized by a strong, broad photoluminescence spectrum. This light emission, centered in the near infrared and extending well into the visible range, has potential applications for the development of photonic materials based on silicon nanostructures. Here, we report on our attempts to form luminescent silica microspheres containing embedded silicon nanocrystals. Arrays of luminescent microspheres were successfully fabricated, without significant coagulation or destruction of the silica spheres during the silicon ion implantation step. However, a substantial deformation on the surface of the spheres that occurred during the high-flux implantation prevented the development of resonant cavity modes in the luminescence spectra. Resonant modes could clearly be observed for pre-implanted and annealed SiO2 wafers with a layer of pristine microspheres subsequently deposited on the implanted surface. These results suggest an alternative method for producing highly durable luminescent silica “microbeads”. At lower ion fluxes, the development of luminescent microsphere superlattices with novel optical properties due to coupling of the light emission from the silicon nanocrystals into the resonant cavity modes may be possible if the deformation effects can be reduced or eliminated.