What controls the crust-mantle connectivity during the early stages of continental-plate boundary development remains poorly constrained. Crustal thinning, lithospheric-scale faults and elevated heat flow are commonly regarded as the main drivers of mantle-fluid transfer, yet their relative importance remains unclear. The Betics (SE Spain) combine all these features in a context of a nascent diffuse plate boundary between Africa and Iberia. We combine noble gas and stable isotope analyses of spring and associated travertines sampled across several crustal- to lithospheric-scale faults. Despite favorable conditions for mantle degassing, mantle-sourced helium is limited to a highly localized zone in the northeastern part of the region, where it accounts for 2 to 6%. Elsewhere, most springs record a ≥99% crustal helium signature, even where the crust is thinnest (≤20 km). Travertines show the clearest thermogenic signatures along the most seismogenic fault of the region. Combined with paleofluid data, this study shows that crust-mantle connectivity shifted from the western and southeastern Betics during the Eocene-Miocene to the northeastern Betics since the Pliocene. This mantle-fluid migration mirrors the localization of present-day seismicity, indicating that active strain partitioning and localized transtension play a key role in sustaining crust-mantle connectivity under an overall compressional regime.