Titanium dioxide (TiO2) nanoparticles (NPs) are widely used in industry and commercial products. Thus, their potential risks to the environment and human health must be evaluated. Doping NPs with certain ions makes it possible to mix properties or generate new ones. Thus, in order to track TiO2 NPs in biological assays, doping with europium (Eu3+) ions was performed, which luminesce in red. Here, we synthesized TiO2 and Eu3+-doped TiO2 nanocrystals (NCs) in anatase phase to verify the toxicity at different concentrations in Drosophila melanogaster and track the distribution of these NCs in vivo. We verified that the incorporation of europium improved the biocompatibility in relation to the pure samples. The presence of Eu3+-doped TiO2 NCs in the gut, brain, and fat body of larvae and intestinal cells of adult animals was detected. Eu3+-doped TiO2 NCs caused significant larval and pupal mortality rates, in addition to leading to the formation of reactive species, especially at high concentrations. Therefore, our data demonstrated it was possible to trace the Eu3+-doped TiO2 NCs, but TiO2 and Eu3+-doped TiO2 NCs in anatase phase were toxic to fruit flies at the tested concentrations, and should be used with caution to minimize health risks.