Nanostructured materials have been widely investigated envisaging biomedical applications, in particular with the aim of selectively carrying drugs or molecules of interest to a target tissue or organ. In this context, boron nitride nanotubes (BNNTs) functionalized with specific moieties have demonstrated to be useful candidates for the delivery of proteins, drugs, and also nucleic acids. In this study, the influence of gum Arabic functionalized BNNTs was evaluated on the differentiation process of mesenchymal stem cells. The nanotubes have been characterized by transmission electron microscopy, scanning electron microscopy, Fourier transform infrared spectroscopy, Raman spectroscopy, and dynamic light scattering. In vitro assays on mesenchymal stem cells were performed to evaluate their cytocompatibility in terms of cell viability and metabolic activity. Interactions cells/nanoparticles were further investigated through the analysis of the cytoskeleton conformation. Finally, the differentiation of mesenchymal stem cells into adipocytes and osteocytes, treated with safe doses of BNNTs, was assessed both at gene and phenotype level.