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Proximity of a topological insulator (TI) surface with a magnetic insulator (MI) can open an exchange gap at the Dirac point leading to exploration of surface quantum anomalous Hall effect. An important requirement to observe the above effect is to prevent the topological breakdown of the surface states (SSs) due to various interface coupling effects and to tune the Fermi level at the interface near the Dirac point. In this work, we demonstrate the growth of high-quality c-axis oriented strain-free layered films of TI, Bi2Se3, on amorphous SiO2 substrate in proximity to an MI, europium sulfide (EuS), that show stronger weak anti-localization response from the surface than previous studies with epitaxially interfaced heterostructures. Importantly, we find gate and magnetic field cooling modulated localization effects in the SSs, attributed to the position of interface Fermi level within the band gap that is also corroborated from our positron annihilation spectroscopy measurements. Furthermore, our experiments provide a direct evidence of gate-controlled enhanced interface magnetism in EuS arising from the carrier mediated Ruderman–Kittel–Kasuya–Yosida interactions across the Bi2Se3/EuS interface. These findings demonstrate the existence of complex interfacial phenomena affecting the localization response of the SSs that might be important in proximity engineering of the TI surface to observe surface quantum Hall effects.