In the hyper-arid deserts of Egypt, where extreme environmental conditions prevail, understanding the symbiotic relationship between the sparse vegetation cover and the underlying soil is crucial for unraveling the mechanisms of plant survival and ecosystem functioning. This study investigates vegetation composition, environmental drivers, and their interactions in an unprotected area of Egypt's northern Eastern Desert, which has recently experienced substantial anthropogenic disturbances. Primary threats to vegetation include road construction, unregulated quarrying, and overexploitation of natural resources. To represent the habitats present in the study area, 20 stands were selected. In each stand, the existing plant species were recorded, soil samples were taken from each stand, and multivariate statistics (DCA) were conducted to show the relationship between the distinctive plant indicators for each stand, as well as the most influential soil factors in each stand. Then, the state of the vegetation cover in previous years (2014) was compared with the state in the study year (2024). A total of 75 plant species were documented, with Asteraceae (15 species) and Fabaceae (6 species) representing the most diverse families. Perennials (73%), chamaephytes (44%), and Saharo-Arabian species (71%) dominated the flora. Detrended Correspondence Analysis (DCA) revealed that the studied stands were divided into four groups (A, B, C, and D). Each group was ecologically similar to the other. Each group of stands had distinctive plant indicators and the soil factors most closely associated with them. Based on the IUCN Red List, conservation status assessments were provided for each species (65 species were unevaluated, while only 11% of the total species are classified as Least Concern, with no taxa appearing in the threatened category). The presence of invasive non-native taxa, such as Beta vulgaris and Centaurea calcitrapa, which threaten native biodiversity, was noted. Analysis of the Soil Adjusted Vegetation Index (SAVI) revealed a reduction in vegetation cover between 2014 (SAVI range: -0.523911 to 0.860437) and 2024 (SAVI range: -0.574714 to 1.08698). The recorded plant species include 16 medicinal plants. Escalating habitat destruction and anthropogenic pressures underscore the urgent need for targeted conservation strategies to safeguard biodiversity in this vulnerable region.