Hydroxyapatite modified with methacrylate groups-bearing polyhedral oligomeric silsesquioxane was for the first time applied as a filler in the experimental composite for dental applications. As the modifier changed the hydroxyapatite surface from hydrophilic to hydrophobic, it was predicted that the stability of the obtained composites would be improved in comparison with raw hydroxyapatite-filled composites. The stability in the oral imitating environment, basic physicochemical properties, and remineralizing potential understood as the ability to release calcium ions, were examined. The distribution of the fillers in the organic matrix, composites’ degree of conversion, depth of cure, flexural and compressive strengths, sorption, and solubility after 2 and 12 weeks of incubation, and the concentrations of calcium released were examined. The results were subjected to statistical analysis. The filler modification resulted in the improvement of the composites’ mass stability during long-term incubation with simultaneous beneficial more balanced calcium release profiles and comparable physicochemical properties.