In this study, we aim to investigate the entropy production in the magnetohydrodynamic (MHD) flow of hybrid nanofluids over permeable rotating disks. We will analyze the entropy production within a three‐dimensional MHD flow of Ag‐MgO nanofluid over a rotating porous disk with variable fluid properties. Our analysis will incorporate time‐dependent radial stretching and slip effects on velocities and temperature. Moreover, the study will take into account exponentially temperature‐dependent viscosity and nonlinear thermal radiation. The study uses self‐similar transformations to convert the coupled nonlinear partial differential equations into a set of nonlinear ordinary differential equations. Numerically solving these equations involves using a shooting technique and relies on the 4th‐order Runge–Kutta–Fehlberg method. The rotation of the disk introduces a parameter that accelerates fluid motion. The study explores heat transfer rate, skin friction, and entropy production quantified by the Bejan number. Various factors, including magnetic field intensity, disk rotation, thermal radiation, and variable viscosity, influence this quantification. The outcomes of the study can enhance system efficiency through suitable parameter choices, deepening our understanding of entropy generation and system performance under varying factors. This research is important for improving heat transfer processes, reducing energy waste, and improving the design and operation of advanced fluid systems in engineering applications. The results could lead to innovations in thermal management, energy conservation, and sustainable engineering practices.