The depositional ages and provenance of the Paleozoic Araba and Naqus Formations along the northern Gondwanan margin in Egypt have remained uncertain due to a lack of index fossils. Resolving this issue is crucial for understanding regional geology during deposition and subsequent tectonic development. We integrate detailed facies analysis, anisotropy of magnetic susceptibility (AMS), paleomagnetism, and mineralogical data to elucidate the genesis and depositional ages of the Araba and Naqus Formations. Petrographic analyses identified seven distinct facies types, providing insights into sedimentary textures, maturity, and sources, with contributions from igneous and metamorphic sources indicated by heavy minerals. X-ray diffraction (XRD) analysis identified accessory minerals such as quartz, goethite, kaolinite, hematite, and anatase. Paleomagnetism isolated two magnetic components (CA and CN) providing the first robust paleo pole positions at Lat. = 70.8° N, Long. = 308.2° E and Lat. = 37.8° N, Long. = 233.1° E, indicating Cambrian and Carboniferous ages for the Araba and Naqus formations, respectively. Thermal demagnetization constrained these dates using established polarity timescales. Mineralogical data indicated that the Araba Formation originated from an igneous source, while the Naqus Formation had a mixed metamorphic-igneous provenance. The integrated AMS and paleomagnetic data reveal evidence of post-depositional deformation. Specifically, the clustering of maximum AMS axes in the NW–SE direction for both formations, suggests the initial presence of a primary depositional fabric. However, prevalent tectonic activity during the Cenozoic appears to have overprinted and modified this fabric through deformation related to rifting of the Gulf of Suez region. Through this novel multi-proxy approach, we have resolved long-standing uncertainties regarding the formations' depositional ages. Our study thereby provides the first chronostratigraphic framework for these strategically important sedimentary units, significantly advancing understanding of regional Paleozoic geology.Graphical abstract