Carbon sequestration in deep saline aquifers was recently developed at the industrial scale. CO2 injection experiences in carbonates are quite limited, most of them coming from projects carried out in porous mediums in the USA and Canada. Hontomín (Spain) is the actual on-shore injection pilot in Europe, being a naturally fractured carbonate reservoir where innovative CO2 injection strategies are being performed within the ENOS Project. CO2 migration through the fracture network existing on site produces hydrodynamic, mechanical and geochemical effectsdifferent from those caused by the injection in mediums with a high matrix permeability. The interpretation of these effects is required to design safe and efficient injection strategies in these formations. For this, it is necessary to determine the evolution of pressure, temperature and flow rate during the injection, as well as the period of pressure recovery during the fall-off phase. The first results from the not-continuous injections (8–24 h) conducted at Hontomín reveal the injection of liquid CO2 (density value of 0.828 t/m3) and the fluid transmissivity through the fractures. Taking into account the evolution of the pressure and flow rate showed variations of up to 23% and 30% respectively, which means that the relevant changes of injectivity took place. The results were modeled with a compositional dual media model which accounts for both temperature effects and multiphase flow hysteresis because alternative brine and CO2 injections were conducted. Advanced modeling shows the lateral extension of CO2 and the temperature disturbance away from the well.