Dental caries and periodontal disease are responsible for the most frequent set of chronic diseases in humans, for which no perfectly regenerative solutions are available yet. As a result, materials combining an intrinsic antibacterial activity with tissue regeneration properties for minimally invasive dental therapies are in high demand. Here we report on the fabrication and characterization of a novel nanocomposite material for such dental applications. The material is composed of narrowly disperse Na2O–CaO–P2O5–SiO2 bioglass-ceramic nanoparticles, 30–70 nm in diameter, doped with antibacterial and osteogenic zinc and niobium ions, and hybridized with chitosan. These systems were characterized for their particle size, morphology, atomic and phase composition, and glass-ceramic/polymer interface with the use of transmission electron microscopy, energy-dispersive X-ray analysis, X-ray diffraction and Fourier transform infrared spectroscopy. After annealing at 680 °C, amorphous silica in the bioglass-ceramic coexisted with silicalite-1 and combeite, the average crystallite size of which was 20–40 nm. In spite of the significantly better incorporation of zinc than of niobium inside the glass-ceramic network, zinc did not affect the particle size and shape distribution, while niobium lowered the average particle size. Chitosan increased the hydration capacity of the bioglass-ceramic and it formed a continuous interface around the bioglass-ceramic nanoparticles, devoid of micropores. This intimacy of the interface was confirmed by the downshift of the critical Si–O(–Si) vibration modes in the bioglass-ceramic upon hybridization with chitosan. The addition of zinc ions hampered the partial recrystallization during annealing by interfering with the Si–O network restructuring, in direct proportion with its concentration. Niobium ions produced a similar structure-breaking effect, which was evidenced, as in the case of zinc, by upshifting the antisymmetric Si–O–Si stretch of the bridging oxygen and increasing the full-width at half maxima for all the major Si–O(–Si) vibration modes. The effective electrostatic attraction between the aminated hydrocarbon chains of chitosan and the negatively charged silanol groups of silica may extend to the interaction with dentin collagen fibrils decalcified due to caries, making the material of potential interest for adhesive fillers of cariogenic lesions in teeth. Both the undoped and the doped bioactive glass-ceramics interacted favorably with odontoblast-like cells, accentuating their potential for further research for applications in minimally invasive reparative dentistry.