The injection of carbon dioxide (CO 2 ) or the non-wetting fluid intrusion into crystalline rock remains being a poorly understood process due to the complexities in characterizing very low permeable and stiff geomaterials. This knowledge gap is critical for enhanced geothermal systems and in-situ carbon mineralization projects where CO 2 may serve as a mobile fluid within fractured crystalline formations. Most of the existing studies rely on numerical simulations with limited experimental validations and do not fully consider the complexity of multi-phase flow. Hereby, we adopt a novel method to evaluate the degree of saturation of the non-wetting fluid in a tight rock with nanometer scale pore sizes from accurate poromechanical and hydraulic measurements, as well as wetting and non-wetting fluid characteristics. We select thermally damaged granite and naturally fractured rhyolite as representative crystalline rock, fully saturate them with water, and perform simultaneous injection of water and liquid CO 2 . The flow properties are measured using the core flooding device that allows observation of multiple fluid flow at controlled rates. CO 2 breakthrough pressures for pressurized fractured crystalline rock are measured to be on the order of 0.1–1 MPa. The exponent values for relative water permeabilities are 1.6 for granite and 1.9 for rhyolite – significantly lower than those typically reported for tight rock, meaning that the fluid flow is mainly governed by the fractures. The exponent values for relative CO 2 permeability are above 5.5, indicating high sensitivity to the degree of CO 2 saturation. Moreover, CO 2 saturation appears to remain below 50%, even when CO 2 is the only injected fluid and its overpressures exceeds 6 MPa. Overall, this study highlights significant limitations in using CO 2 as a working fluid for geoenergy projects in crystalline rock.