The symmetry of the theory of relativity under diffeomorphisms strongly depends on the equivalence principle. Violation of Equivalence Principle (VEP) can be tested by looking for deviations from the standard framework of neutrino oscillations. In recent works, it has been shown that strong constraints on the VEP parameter space can be placed by means of the atmospheric neutrinos observed by the IceCube neutrino telescope. In this paper, we focus on the KM3NeT neutrino telescope and perform a forecast analysis to assess its capacity to probe VEP. Most importantly, we examine the crucial role played by systematic uncertainties affecting the neutrino observations. We find that KM3NeT will constrain VEP parameters times the local gravitational potential at the level of 10−27. Due to the systematic-dominated regime, independent analyses from different neutrino telescopes are fundamental for robustly testing the equivalence principle.