Non-trivial spin textures driven by strong exchange interaction, magneto-crystalline anisotropy, and electron correlation in a low-dimensional magnetic material often lead to unusual electronic transitions. Through a combination of transport experiments in exfoliated nanoflakes down to 16 layers and first principle calculations, we unravel emergent electronic phases in quasi-2D van der Waals ferromagnet, Fe4GeTe2, possessing ferromagnetic TC ~ 270 K, along with a spin-reorientation transition (TSR ~ 120 K) with the change of magnetic easy axis. Two electronic transitions are identified. The first transition near TSR exhibits a sharp fall in resistivity, followed by a sign change in the ordinary Hall coefficient (R0), together with, maximum negative magnetoresistance (MR) and anomalous Hall conductivity. Another unusual electronic transition, hitherto unknown, is observed near ~ 40–50 K (TQ), where R0 again changes sign and below which, the resistivity shows a quadratic temperature dependence, and MR becomes positive. An analysis of the experimental data further uncovers the role of competing inelastic scattering processes in anomalous magnetotransport behavior. The density-functional theory based first-principle calculations unveil two possible magnetic phases, followed by a low-energy model Hamiltonian which captures the essence of these phases as well as explains the observed magnetotransport behavior. Thus, we demonstrate an interplay between magnetism and band topology and its consequence on electron transport in Fe4GeTe2, important for spintronic applications.