Over the last century, the state of stress in the earth’s upper crust has undergone rapid changes because of human activities associated with fluid withdrawal and injection in subsurface formations. The stress dependency of multiphase flow mechanisms in earth materials is a substantial challenge to understand, quantify, and model for many applications in groundwater hydrology, applied geophysics, CO2 subsurface storage, and the wider geoenergy field (e.g., geothermal energy, hydrogen storage, hydrocarbon recovery). Here, we conduct core-scale experiments using N2/water phases to study primary drainage followed by spontaneous imbibition in a carbonate specimen under increasing isotropic effective stress and isothermal conditions. Using X-ray computed micro-tomography images of the unconfined specimen, we introduce a novel coupling approach to reconstruct pore-deformation and simulate multiphase flow inside the deformed pore-space followed by a semi-analytical calculation of spontaneous imbibition. We show that the irreducible water saturation increases while the normalized volume of spontaneously imbibed water into the specimen decreases (46–25%) in response to an increase in effective stress (0–30 MPa), leading to higher residual gas saturations. Furthermore, the imbibition rate decreases with effective stress, which is also predicted by a numerical model, due to a decrease in water relative permeability as the pore-space becomes more confined and tortuous. This fundamental study provides new insights into the physics of multiphase fluid transport, CO2 storage capacity, and recovery of subsurface resources incorporating the impact of poromechanics.