In felsic igneous rocks, the parent and daughter elements in the widely used Sm–Nd and Lu–Hf isotope tracer systems are mainly hosted in accessory phases. Recrystallisation and/or breakdown of these minerals during metamorphism, deformation and weathering potentially compromises the chemical and isotopic composition of the respective whole rocks, impeding the utility of such information for deducing the timing, rates and processes of crust-mantle differentiation in the early Earth. The different abilities of zircon and REE-rich minerals to withstand metamorphism have been suggested as a reason for the decoupling of the Lu–Hf and Sm–Nd isotope systems observed in a number of ancient gneiss terranes. The controls on element mobility and subsequent isotopic disturbance during recrystallisation and breakdown of LREE-rich accessory minerals are, however incompletely understood. Here, we use petrography, element mapping, and microanalysis of accessory minerals, in tandem with whole rock Sm–Nd data, to assess the reliability of the Sm–Nd system in the 3.59–3.58 Ga Mount Webber Gabbros, the oldest rocks in the Pilbara Craton (Western Australia). We show that despite multiple thermal events, which reset the mineral Sm–Nd systematics, and decomposition of the REE-rich mineral allanite, the Mount Webber rocks retained the Sm–Nd isotope signatures of their magmatic protoliths at the whole-rock scale. We show that the allanite breakdown occurred during modern, near-surface weathering processes at low temperature, such that the REE were sequestered into secondary minerals rather than escaping in higher temperature metamorphic fluids. The whole rock Sm–Nd, and zircon O–Hf signatures, together with new 142Nd isotope data, suggest derivation of the Mount Webber rocks from undifferentiated mantle sources that preserve no evidence for Hadean silicate Earth differentiation. This study highlights the benefits of a combined analytical approach using both in-situ and whole-rock isotope analyses to obtain a more complete record of the source and thermal evolution of ancient, highly metamorphosed igneous rocks.