© 2021, The Author(s). The role of nanofluids is of fundamental significance in the cooling process of small electronic devices including microchips and other associated gadgets in microfluidics. With such astounding applications of nanofluids in mind, it is intended to examine the flow of magnetohydrodynamic nanofluid comprising a novel combination of multi-walled carbon nanotubes and engine oil over a stretched rotating disk. The concentration equation is modified by considering the autocatalytic chemical reaction. The succor of the bvp4c numerical technique amalgamated with the response surface methodology is secured for the solution of a highly nonlinear system of equations. The sensitivity analysis is performed using a response surface methodology. The significant impacts of the prominent arising parameters versus involved fields are investigated through graphical illustrations. It is observed that the skin friction coefficient and local Nusselt number are positively sensitive to nanoparticle volume fraction while it is positively sensitive to the suction parameter. It is negatively sensitive to the Magnetic parameter. The skin friction coefficient is negatively sensitive to all input parameters.