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Long-standing arguments regarding the early cultural transition, the domestication of plants and the impacts of climate change on past Egyptian societies remain contentious. In this paper, we demonstrate that grazing started at our study site, Kom El-Khilgan in the NE Nile Delta, ca. 7000 years ago, which was several hundred years prior to crop farming. We examined pollen-spores and non-pollen palynomorphs (NPP) in a 1-m-deep sediment profile (KH-1) in the study site, defined archaeologically as the Pre-Dynastic (>5.9 ka) in age. Our results show that before ca. 7.0 ka, major floods prevailed in the Nile Delta, as highly-concentrated Podocarpus and Polypodiaceae were transported from the East African highlands and Cyperaceae of higher Nile flow indication. This humid phase was succeeded by a brief period of drying climate ca. 7.0–6.6 ka, allowing the entry of the first settlers who commenced grazing their animals on previously inundated wetlands. This change is indicated by the remarkable increase in fungal spores (Cercophora, Sordaria, Coniochaeta cf. Ligniaria) from accumulations of animal dung. At ca. 6.6 ka, the abrupt appearance of domesticated cereal pollen (Poaceae >35 μm) and cereal grass pathogens (Pericornia and Sorosporium) suggests an amelioration of the climate that allowed the introduction of cereal crops and related water management activities. Grazing and cropping co-existed for the remainder of the record during the time when there occurred a mega-tendency of climate drying towards recent time. A drought event recognized ca. 4.2 ka led to the collapse of the Old Kingdom.