This article explores the impact of binary chemical reactions with activation energy on the flow of magnetized mono and hybrid nanofluids within a porous artery under the effects of viscous dissipation, nonlinear thermal radiation, and Joule heating. The main novelty of this study lies in considering a non-Newtonian Ellis fluid model of blood through a stretching stenotic artery consisting of gold (Au) and silver (Ag) nanoparticles. Additionally, velocity slip, convective temperature, and concentration boundary conditions are applied at the arterial surface. The proposed model compares the performance of Ag/Blood nanofluid and Au-Ag/Blood hybrid nanofluid models. The governing equations are solved using the bvp4c built-in solver in MATLAB, which employs advanced numerical techniques and algorithms tailored for BVPs, ensuring quicker convergence with minor errors and accurate solutions. Graphs are plotted for concentration, temperature, velocity, entropy minimization, skin friction coefficient, Nusselt number, and Sherwood number for various physical parameters. The results show that with increased nonlinear thermal radiation (0.1≤Nr≤2.0), thermal Biot number (0.1≤Bi1≤0.3), and Eckert number (0.01≤Ec≤0.2), the thermal distribution profile exhibits a rising trend. In contrast, with increasing fluctuations in the chemical reaction rate parameter (0.1≤Rc≤0.3) and Schmidt number (1.0≤Sc≤3.0), the concentration distribution profile exhibits a decreasing trend. In terms of mass and heat transfer efficiency, the Au-Ag/Blood hybrid nanofluid flow outperforms the Ag/Blood nanofluid model. More entropy is observed for Au-Ag/Blood compared to Ag/Blood in the stenotic artery. Heat energy may be created by targeting the injured area and avoiding harm to nearby tissues. Localized heating can widen arteries and increase blood flow to the affected locations, potentially aiding cardiovascular health management and personalized therapy. This study has various implications for the design of drug delivery systems, biophysical models, innovative materials, and our knowledge of fluid dynamics and heat transfer. However, nanofluid/hybrid nanofluid stability is challenging for current researchers since this modeled flow can be considered over a shrinking artery or in the trihybrid model in future studies.