In this article, the study of chemical reaction and heat generation effects on the magnetohydrodynamic free convection in the thermal and mass stratified fluid-filled porous enclosure under the influence of cross-diffusion forces is extended to the entropy generation analysis for the design of relevant tools of engineering applications. Here, the multiphysics associated with natural convection in doubly stratified fluid containing chemically reactive square porous enclosure under uniform magnetic field furnishes novel flow dynamics modeling. Since the distinctive nature of the free convective flow mechanism is described by the complex heat and mass transfer process, the thermal investigation cannot be considered complete until the visual illustration of the transportation of heat and mass flux is provided. Therefore, the new heat flux and mass flux models are proposed for the multi-force effect on chemically reactive porous media under the effect of viscous dissipative heat generation to facilitate the directional manifestation of heat and mass flux transitions along with intensity. Additionally, the thermodynamical measures are established by the new entropy generation model and advanced Bejan number irreversibility characterization.