<p>Magnetic Tunnel Junctions (MTJs) operate on the principle of spin-dependent tunneling through an ultrathin insulating barrier, and their magnetoresistive response depends on the relative alignment of magnetization within the two ferromagnetic layers. In this work, the free-layer thickness controls the magnetization states and magnetotransport behavior of CoFeNi/MgO/CoFeNi MTJs by means of micromagnetic simulations. The findings show a clear transition in thickness from coherent single-domain rotation towards vortex-mediated reversal. This transition, in turn, directly controls the Tunneling Magnetoresistance (TMR) observed to change in polarity from +199% at 25 nm to −344% at 100 nm. The coercive field moderately increases from 22.3 mT to 24.9 mT as a function of thickness, which attests to the transition between uniform and non-collinear magnetization configurations. Thus, the polarity inversion in sign arises from the formation of vortex states at larger thicknesses, which create non-collinear interfacial spin alignments and enhanced spin-flip tunneling, resulting in the reversal of the effective spin polarization. The research provides systematic insights into the thickness-dependent magnetic configurations, energy landscapes, and transport behavior in CoFeNi-based MTJs, with conclusions important for further prospective memory and logic devices.</p>