Conjugated polymer nanodots are shown to have great potential as probe for fluorescence-based biosensing and bioimaging applications. Yet the need to functionalize these polymer nanodots is hindering their uses in many applications. Here, we report the preparation and encapsulation of fluorescent polymer nanodots inside silica nanoparticles. The facile, template-assisted method has little effect on the fluorescent properties of polymer nanodots. The resulting nanodot-embedded silica nanoparticles can be easily functionalized for downstream applications.