Cross-linking of biocompatible ligand shells significantly improves the stability of nanocrystals in the biological environment. We report a detailed spectroscopic study of radical initiated reactions on poly(isoprene)-b-poly(ethelene glycol) encapsulated CdSe/CdS/ZnS core-shell-shell quantum dots. It was found that the radicals not only initiate cross-linking of the polyisoprene moieties but also may anneal the nanocrystal surfaces and improve their crystallinity.