(1) Background: the current study investigated three nanohybrid composites: two commercial products ClearfilMajestyTM (CM) and HarmonizeTM (HU), compared with an experimental product PS2. (2) Methods: Two sample types were molded using Teflon dies. The first sample type was represented by standard discs (20 mm diameter and 2 mm thickness) (n = 60, 20/each material), used for surface conditioning investigation, specifically roughness monitoring and color stability analysis using AFM and the CIELab test, respectively. The second sample type was a standard cylindrical specimen (4 mm diameter and 6 mm height) for compression testing (n = 60, 20/each material). After complete polymerization, the samples were ground with sandpaper and further polished. The filler size and distribution in the polymer matrix were investigated with SEM. Data were statistically analyzed using the Anova Test followed by Tukey’s post hoc test on the Origin Lab 2019 software produced by OriginLab Corporation, Northampton, MA, USA. (3) Results: A mono-disperse system was identified in HU samples, while CM and PS2 revealed both nano- and microfiller particles. The samples’ observation after immersion in coffee and tea indicated that a lower roughness combined with optimal filler lamination within the polymer matrix assured the best color preservation. The compression strength was lower for the HU sample, while higher values were obtained for the complex filler systems within CM and PS2. (4) Conclusions: the behavior of the investigated nanohybrid composites strongly depends on the microstructural features.