Induced seismicity poses a challenge to the development of Enhanced Geothermal Systems (EGS). Improving monitoring and forecasting techniques is essential to mitigate induced seismicity and thereby fostering a positive perception of EGS projects among local authorities and population. Induced seismicity is the result of complex and coupled thermo-hydro-mechanical-chemical mechanisms. Injection flux and pressure are crucial controlling parameters for both hydraulic stimulation and circulation protocols. We develop a methodology combining a hydro-mechanical model with a seismicity rate model to estimate the magnitude and frequency of mainshocks and aftershocks induced by fluid injection. We apply the methodology to the case of the Basel EGS (2006, Switzerland) to compare the effects of progressive, cyclic and constant injections on the mechanical response of discrete faults. Results from the coupled hydro-mechanical models show that the pore pressure diffusion and consequent enhancement of fault permeability are limited to the vicinity of the injection well during cyclic injection. Additionally, constant injection induces seismicity from the start of the injection but enhances the permeability of most of the faults within a shorter duration, inducing less post-injection seismicity. The methodology can be adapted to any numerical model and allows new projects to be developed by anticipating the safest injection protocol.This article is part of the theme issue Induced seismicity in coupled subsurface systems.