We investigate the microtextural, microchemical, and isotopic effects of late-stage ductile deformation in quartzite mylonites and kyanite–muscovite–quartz veins from the Raft River shear zone (Utah). Quartz microstructures record pervasive disequilibrium, expressed by unannealed features including undulatory extinction, deformation lamellae, and poorly defined fabrics, typical of waning deformation in shear zones. Microchemical disequilibrium is best preserved in kyanite quartzites, where CL-zoned kyanite records repeated fractures, overgrowth, and mineral precipitation, and in muscovite from muscovite-poor quartzite mylonites that shows minor-element zoning consistent with syn-deformational overgrowth on detrital cores. In contrast, muscovite from muscovite-rich kyanite quartzites exhibits minimal chemical zoning. These microchemical variations correlate with ⁴⁰Ar/³⁹Ar age systematics. Chemically zoned muscovite preserves variable single-step ages, including ∼150 Ma ages, reflecting retention of detrital cores. In contrast, syndeformational muscovite consistently yields Miocene ages, indicating recrystallization and new growth below argon closure temperatures that reset inherited isotopic signatures. Similar trends are observed in quartzite mylonites, where increasing quartz recrystallization and stronger crystallographic preferred orientations occur toward deeper structural levels. Together, these observations indicate increasing retrograde deformation and recrystallization with depth in the Raft River shear zone and demonstrate that strain-driven recrystallization exerts a first-order control on muscovite ages. We suggest that apparent thermochronologic gradients in retrograde shear zones may reflect recrystallization gradients rather than temperature gradients. Where cooling limits the thermal driving force for recrystallization, isotopic relics are preserved, and local deformation and fluid availability control re-equilibration. Consequently, isotopic disequilibrium—particularly in the ⁴⁰Ar/³⁹Ar system—may be the rule rather than the exception of retrograde tectonic environments.