<p>Nanofluids have extensive applications and are utilized in technology, science, biomechanics, chemical industries and considerably many more. Motivated by this, the flow of a two-phase nanofluid model with mass and heat transfer over the unsteady mixed convective gyrating cone via a permeable medium subjected to thermal radiation, heat generation and chemical interaction is the focus of this study. The current model is based on inclusive nonlinear partial differential equations (PDEs), which are then renewed using similarity transformations into a comprehensive system of nonlinear ordinary differential equations (ODEs). The solutions of this system are obtained via the finite element approach. The computational results reveal that the cone rotation restrained the secondary flow structures, initiates fluid radial motion and alters the velocity profile. The magnetic field prudently affects the velocity as well thermal boundary layers and boosts the thermal regulation in the nanofluid system. The Brownian motion and thermophoresis jointly modulate nanoparticle propagation and concentration profiles close to the cone wall. The chemical reaction provides more insight into the concentration profile, especially in reactive or industrial fluid systems. Finally, validation has been conducted with existing literature and observed that our methodology exhibited good accuracy. Thus, the study configuration is applicable in biomedical transport, solar energy systems, industrial cooling, and reactive fluid technologies.</p>