Calcium phosphate nanoparticles are highly biocompatible and biodegradable in bone regeneration. On the other hand, strontium and magnesium enhance the formation of bone. The substitution of calcium by strontium and magnesium is an efficient way to improve the biological properties of calcium phosphate-based biomaterials. Strontium-doped calcium phosphate nanoparticles and magnesium-doped calcium phosphate nanoparticles with degrees of cation substitution of 5, 10, 15, and 20 mol% with respect to calcium were prepared by precipitation, followed by surface functionalization with polyethyleneimine (PEI, cationic) or carboxymethylcellulose (CMC, anionic). The nanoparticles were characterized by dynamic light scattering (DLS), zeta potential measurement, scanning electron microscopy (SEM), atomic absorption spectrometry (AAS), energy dispersive X-ray analysis (EDX), and X-ray powder diffraction (XRD). The particles were approximately spherical (diameter 40–70 nm). The addition of magnesium and strontium considerably decreased the internal crystallinity, i.e., the doped particles were almost X-ray amorphous. The cell-biological effects were assessed on three different cell lines, i.e., HeLa cells, MG63 cells, and MC3T3 cells. Cell viability tests (MTT) showed a low cytotoxicity, the alkaline phosphatase (ALP) activity was strongly increased, and the nanoparticles were taken up well by the three cell lines.