The novelty of this study consists of the formulation and characterization of three experimental bleaching gels with hydroxylapatite oxides and fluorine (G28®, G29®, G30®) based on natural fruit extracts compared to the commercial Opalescence 15% (GC, Ultradent, South Jordan, UT, USA). Studies have been conducted on the effect that the experimental bleaching gels have on the color and morphology of different restorative materials (Nanofill®-Schulzer, P.L. Superior Dental Materials GmbH, Hamburg, Germany, and experimental nanocomposites (P11®, P31®, P61®)), immersed in coffee and artificial saliva (for 10 days and 30 days). The study also includes a cytotoxicity test on the gels and nanocomposites after bleaching, with ISO 109993-5 protocols on human dental follicle stem cells. UV-VIS spectroscopy, computerized measurement, and fluorescence spectrometry were used in order to observe the color changes, while the microstructure of the surface was investigated by Scanning Electron Microscopy (SEM). All of the samples immersed in coffee showed the highest color shift in comparison to the baseline. The color difference ΔE values obtained using the two methods (UV-Vis, computerized based on digital images) both after coloring and bleaching, respectively, were different for all four types of nanocomposites stored in the coffee, while no difference was observed in those stored in artificial saliva. The studied experimental gels and nanocomposites had a low cytotoxic effect on cell cultures after bleaching.