Altered crystalline rocks occur at the peneplain exposed in southern Israel and in other localities across North Africa and Arabia where they underlie an extensive blanket of Cambro–Ordovician sandstones. This study focuses on the petrography, mineralogy and geochemistry of top basement rocks of the northern Arabian-Nubian Shield. The altered rocks are shown to be weathering profiles that can be subdivided into three horizons interpreted as apparently unweathered granite, or saprock, which grades upwards to a saprolite, topped by a thin clayey plasmic zone. The plasmic zone is enriched in iron and aluminium and is depleted in silicon, calcium, magnesium and potassium relative to the underlying saprolite. The chemical index of alteration increases upward, but does not exceed 90 and, therefore, lags behind values observed in strongly leached present-day tropical soils. Petrographic examinations reveal iron mobility under local fluctuating redox conditions, similar to modern and Proterozoic soils. A variety of birefringence fabrics induced by shrinkage and expansion of clays during wetting and drying cycles and clay illuviation strongly indicate pedogenic processes rather than a post-depositional alteration. Illite and ordered illite-smectite phases coexist with smectitic illite-smectite in the lower part of the saprolite and with kaolinite in the plasmic zone, in line with increasing chemical index of alteration. Observations are in accordance with the current profile being a remnant of a thick weathering profile whose top was truncated by fluvial incision just prior to deposition of the overlying Early Cambrian sequence. A previously documented Devonian thermal event reaching temperatures of at least 200°C overprinted the studied rocks. During burial diagenesis, illitization affected original smectite rather than kaolinite. However, in spite of the elevated temperatures, illitization was incomplete implying restricted potassium addition. The sub-Cambrian weathering reflects warm and humid conditions in a tropical or sub-tropical climate, in line with several plate reconstructions placing Israel at low latitudes during Cambrian time.