The effect of magnesium fluoridated hydroxyapatite nanoparticles (Mg-FHA NPs) as ceramic species on the morphology, thermal and in vitro bioactivity properties of sodium alginate (SA) matrix was investigated. Preparation of cross-linked SA/FHA bio-nanocomposites (bio-NC)s was carried out under ultrasonic irradiations as fast and green conditions followed by cross-linking with CaCl2. The sonication influence on the dispersion of Mg-FHA in the alginate was studied thoroughly. Morphology images showed that the size of Mg-FHA NPs in the matrix reduced, considerably and the mean diameter of particles was estimated to be about 4 nm. The thermal stability of the alginate did not show significant changes by loading of 2, 6, and 10 wt% of Mg-FHA NPs. The bio-NCs exhibited the good ability of the formation of apatite in simulated body fluid. Mg-FHA growth on the surface of the samples was proved by a noteworthy increase in the phosphate absorption bands in FT-IR spectra, which shows the potential application of the obtained bio-NCs in tissue engineering.