The Morro Vermelho Cave (MVC) (Brazil) developed within the Morro Vermelho karst system, which affected Neoproterozoic limestones (Salitre Formation). The MVC experienced little interactions with meteoric processes and is an example of a hypogenic cave formed during strike-slip deformation. The Salitre carbonates in the MVC experienced distributed deformation along an elongated domain overlying a buried strike-slip fault. Gently dipping, semiductile shear zones formed with decimeter-scale (3.9 in.) dolomitic veins. In our model, Mg-rich fluids flowing along the Salitre aquifer caused at the same time extensive dolomitization of the body of rock (100-m [328-ft] scale) experiencing distributed deformation. With progressive displacement, the deep strike-slip fault propagated upward causing the development of an anticline pop-up, steepening sedimentary layers, and steep 1–10-m-long (3.3–33.8-ft) fractures, which served as pathways for upward fluid flow. These steep extensional fractures made it possible for fluids flowing in lower, quartzitic aquifers to enter the carbonate aquifer causing silica deposition in rock cavities and in fractures and fault planes. Following the main stage of speleogenesis, silica deposition took over again depositing on the cave walls a continuous silica crust, rarely observed in other settings worldwide. The interplay between regional bedding-parallel flow and focused circulation of fluids along steep faults and dipping layers, and the associated rock–fluid interactions are not unique to the contractional settings presented but can also occur in association with similar faults in rifted continental margins.