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Carbon Capture and Storage (CCS) projects are designed to capture CO₂ from high-emission industrial sources and inject it into deep geological formations, including saline aquifers and depleted hydrocarbon reservoirs. A critical barrier is demonstrating the safe, large-scale, and long-term containment of injected CO₂. Injection into deep subsurface formations alters the reservoir’s thermal, hydraulic, chemical, and mechanical conditions, highlighting the importance of modelling the coupled interactions among the injected CO₂, the host rock, and the formation fluids. Despite advances in geomechanical and CO₂ flow modelling aimed at representing these processes, many studies still rely on soft-coupling strategies and simplified assumptions, which limit the reliable assessment of induced hazards and the prediction of CO₂ plume evolution. As a result, such models often fail to capture the inherently 3D redistribution of stress and strain localisation, struggling to reproduce realistic in situ stress-path behaviour and the hysteretic responses documented in depleted fields and laboratory experiments. Capturing reliable stress-dependent behaviour through coupled stress-flow modelling becomes particularly challenging in naturally fractured, heterogeneous-layered carbonate reservoirs, where these limitations are amplified by strong spatial variations in hydromechanical properties arising from facies variability, diagenetic processes, and complex structural settings. Early diagenetic lithification imparts variable mechanical competence and fracture susceptibility during shallow burial, while depositional heterogeneity related to facies fabrics enhances mechanical anisotropy. Moreover, natural fracture networks and fault-rock properties exert a first-order control on fluid circulation and stress transfer, with aperture, stiffness, and permeability evolving dynamically in response to changes in effective stress. In this study, we present fully coupled, critical-state geomechanical–multiphase flow simulations of CO₂ injection in naturally fractured, layered carbonate reservoirs representative of aquifers and depleted carbonate systems found in Brazil. The workflow integrates descriptive and quantitative analyses from a Brazilian subsurface microbial carbonate reservoir and (ii) a Brazilian analogue carbonate outcrop. Our modelling framework couples matrix-controlled poro-elasto-plastic deformation with fracture-dominated flow, enabling assessment of stress-path evolution, pore-pressure build-up, and associated changes in saturation and porosity during CO₂ injection. Critical-state models are constrained using laboratory triaxial test data, while multiscale fracture-network connectivity derived from carbonate outcrop analogues is used to constrain dense embedded-fracture continuum representations.