The increasing relevance of nanofluids in biomedical heat and mass transfer applications has driven the need for more biologically realistic models that can accurately represent the micro-scale dynamics of blood flow. Motivated by this need, this research introduces a novel bio-convective formulation by coupling the effects of nanoparticle-enhanced conductivity with microorganism-induced convection, providing a comprehensive theoretical framework for bioconvective transport of non-Newtonian bio-nanofluids over a nonlinear stretching surface. The model is intended as an idealized representation of shear-driven transport mechanisms relevant to microfluidic and bio-inspired thermal systems. The governing boundary-layer equations for momentum, energy, and microorganism concentration are transformed via similarity variables and solved numerically using the Runge–Kutta–Fehlberg (RKF45) method with the shooting technique. The results reveal that the inclusion of motile microorganisms significantly modifies the flow structure, reducing their accumulation near the surface with increasing nanoparticle concentration, radiation, and magnetic effects. Comparisons between gold and silver-based nanofluids reveal that gold-based suspensions maintain higher thermal energy levels, accompanied by increased viscous resistance and diminished microorganism transport. Parametric analyses indicate that higher nanoparticle concentrations and magnetic field strength lead to reduced velocity and microorganism density, while enhancing the fluid’s temperature due to augmented viscous and Joule heating. Furthermore, increasing the nonlinear stretching parameter and Prandtl number improves convective cooling but restricts microorganism transport. While biomedical applications are discussed for motivation, the present configuration does not represent a patient-specific arterial geometry.