Subduction-zone fluid–rock interactions have a direct impact onto elemental and isotopic homogeneity of progressively buried and exhumed crustal lithologies by providing an interface for local mass-transfer and enhancing metamorphic reactions. In order to assess the scales of fluid mobility, chemical and isotopic inheritance, as well as resulting degrees of isotopic heterogeneity in the exhumed high-pressure lithologies, we performed the detailed mineralogical, in-situ trace-element and Rb–Sr isotope studies, combined with P–T–X thermodynamic modelling of representative eclogites from the Alag Khadny accretionary complex (SW Mongolia). The eclogites (garnet + omphacite + phengite + rutile + quartz + retrograde amphibole and clinozoisite) display records of subduction-related burial to 540–625 °C and 1.7–2.1 GPa, with the enclosed phengite supposed to be in equilibrium at prograde-to-peak conditions. Trace-element signatures, including Cs/Rb (0.03–0.08) and Ba/Rb (7.1–13.8) ratios of phengite, are consistent with moderately to strongly altered protoliths of eclogites, which is supported by elevated δ18O values and in-situ Rb–Sr constraints on the initial (87Sr/86Sr)I ratios of phengite within 0.70549–0.70957. Partial backward rehydration (~ 0.5–1.0 wt% of H2O added) during decompression from 1.6 to 1.2 GPa produced amphibole- and clinozoisite-bearing assemblages, did not significantly affect LILE systematics and variable 87Rb/86Sr ratios of phengite. Limited Rb and Ba loss from phengite during recrystallization is suspected in the evidently deformed eclogites based on the LILE mineral–fluid and phengite–amphibole partitioning data. No exclusive evidence is found in amphibole for LILE-rich metasedimentary fluid with high (87Sr/86Sr)I released into eclogites. Instead, unradiogenic 87Sr/86Sr (0.70279–0.70301) of clinozoisite highlights metasomatic addition from the underlying mafic crust or dehydrated peridotitic mantle. Variable deformation-enhanced fluid-rock interaction during early exhumation was recorded by in-situ phengite Rb-Sr geochronology at 568 ± 9 Ma, which is considered a direct fluid flow snapshot and place a new minimum age constraint for the peak subduction burial. We argue that, except cases of apparent metasomatic origin of phengite, its (87Sr/86Sr)I ratios may be a sensitive tracer for the eclogite precursor alteration due to limited Sr mobility. Sample-scale Rb-Sr isotopic heterogeneities may be preserved in the orogenic eclogites due to multi-stage retrograde hydration and should be taken into account while interpreting the bulk-rock Sr isotope data.