The permeability of fault zones plays a significant role on the distribution of georesources and on seismogenesis in the brittle upper crust, where both natural and induced seismicity are often associated with fluid migration and overpressure. Detailed models of the permeability structure of fault zones are thus necessary to refine our understanding of natural fluid pathways and of the mechanisms leading to fluid compartmentalization and possible overpressure in the crust. Fault zones commonly contain complex internal architectures defined by the spatial juxtaposition of “brittle structural facies” (BSF), which progressively and continuously form and evolve during faulting and deformation. We present the first systematic in-situ outcrop permeability measurements from a range of BSFs from two architecturally complex fault zones in the Northern Apennines (Italy). A stark spatial heterogeneity of the present-day permeability (up to four orders of magnitude) even for tightly juxtaposed BSFs belonging to the same fault emerges as a key structural and hydraulic feature. Insights from this study allow us to better understand how complex fault architectures steer the 3D hydraulic structure of the brittle upper crust. Fault hydraulic properties, which may change through space but also in time during an orogenesis and/or individual seismic cycles, in turn steer the development of overpressured volumes, where fluid-induced seismogenesis may localize.