We analysed gabbroic and dioritic rocks from the Atud igneous complex in the Eastern Desert of Egypt to understand better the formation of juvenile continental crust of the Arabian–Nubian Shield. Our results show that the rocks are the same age (U–Pb zircon ages of 694.5 ± 2.1 Ma for two diorites and 695.3 ± 3.4 Ma for one gabbronorite). These are partial melts of the mantle and related fractionates (εNd690 = +4.2 to +7.3, 87Sr/86Sri = 0.70246–0.70268, zircon δ18O ∼ +5‰). Trace element patterns indicate that Atud magmas formed above a subduction zone as part of a large and long-lived (c. 60 myr) convergent margin. Atud complex igneous rocks belong to a larger metagabbro–epidiorite–diorite complex that formed as a deep crustal mush into which new pulses of mafic magma were periodically emplaced, incorporated and evolved. The petrological evolution can be explained by fractional crystallization of mafic magma plus variable plagioclase accumulation in a mid- to lower crustal MASH zone. The Atud igneous complex shows that mantle partial melting and fractional crystallization and plagioclase accumulation were important for Cryogenian crust formation in this part of the Arabian–Nubian Shield.Supplementary material: Analytical methods and data, calculated equilibrium mineral temperatures, results of petrogenetic modeling, and cathodluminesence images of zircons can be found at https://doi.org/10.6084/m9.figshare.c.4958822