Surface-functionalized vitamin B12 (VB12) biocompatible nanoparticles exploit the well-characterized uptake pathway of VB12, shielding it from enzymatic degradation and inadequate absorption. In this perspective, subsequent to escalated mucus interaction and diffusion analysis, the nanoparticles were investigated by immunostaining with the anti-CD320 antibody, and their internalization mechanisms were examined by selectively blocking specific uptake processes. It was observed that their internalization occurred via an energy-dependent clathrin-mediated mechanism, simultaneously highlighting their remarkable ability to bypass the P-glycoprotein efflux. In particular, the synthesized nanoparticles were evaluated for their cytocompatibility by analyzing cellular proliferation, membrane viscoelasticity, and fluidity by fluorescence recovery after photobleaching and oxidative-stress detection, making them well-suited for successful translation to a clinical setup. Our previous in vitro antileishmanial results were paramount for their further in vivo and toxicity analysis, demonstrating their targeted therapeutic efficiency. The augmented surface hydrophilicity, which is attributed to VB12, and monomerization of amphotericin B in the lipid core strengthened the oral bioavailability and stability of the nanoparticles, as evidenced by the fluorescence resonance energy transfer analysis.