A highly-fractionated garnet-bearing muscovite granite represents the marginal granitic facies of the Abu-Diab multiphase pluton in the Central Eastern Desert of Egypt. New electron microprobe analyses (EMPA) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) data from garnets are reported, in order to constrain their origin and genesis. Garnet in the Abu-Diab host granite is euhedral to subhedral, generally homogeneous and, in rare cases, it shows weak zonation. The garnet contains appreciable amounts of MnO and FeO, with lesser amounts of MgO and CaO, yielding an end-member formula of Sps61–72Alm25–35Prp1–4Adr0–1. Moreover, it is depleted in large ion lithophile elements (LILE) with lower values of Ba, Nb and Sr relative to the primitive mantle. Additionally, it contains high concentrations of HREE and Y and their REE pattern shows strong negative Eu anomalies. The garnet was crystallized under relatively low temperature (646°C–591°C) and pressure (< 3 kbar) conditions. The textural and chemical features indicate that the garnet is magmatic in origin and is chemically similar to that from highly-fractionated A-type granite. It was probably formed at the expense of biotite in a highly-evolved MnO-rich magma and/or by hydroxyl complexing of Mn during the ascending fluid phases.