Over the past four decades, rapid urbanization has profoundly affected the sustainability of urban and peri-urban agriculture (UPA) as well as the diversity of native fruit tree ecotypes. Despite the ecological and agricultural importance of Tunisia’s coastal regions, few studies have addressed the impacts of urbanization on local fruit tree diversity and orchard dynamics. To fill this gap, the present study employs remote sensing to map and quantify the evolution of urban expansion and the degradation of almond orchards between 1980 and 2023. In addition, field surveys were conducted to complement the spatial analysis and to assess the economic, social, and ecological importance of UPA, here defined as all agricultural activities carried out within and around urban areas. These surveys also provided insights into the effects of urbanization on almond cultivation. Cartographic analyses reveal a marked transformation of the landscape under the pressure of urbanization. In Kalâa Kebira, tree crops decreased from 3,234.2 ha in 1980, with a loss of 621 ha by 2023, while urban areas expanded from 145 ha to 1,307.2 ha. In Bouficha, almond and olive plantations declined by 29.4% between 1980 and 2012 (from 11,927.32 ha to 8,420.9 ha), before recovering to 10,666.19 ha by 2023, despite urbanization reaching 1,130.69 ha. This regeneration can be attributed to the central economic role of agriculture (accounting for 80% of local income), government-supported irrigation projects, and the engagement of a new generation of farmers. Field surveys highlight the high genetic diversity and good conservation status of native almond ecotypes in the Kalâa Kebira region, reflecting traditional management practices that safeguard local genetic resources. This diversity represents an asset for adapting to climatic constraints, particularly drought. Conversely, in Bouficha, the expansion of orchards through the introduction of selected or imported almond varieties has led to a reduction in local genetic variability. This process has intensified genetic erosion, already exacerbated by rapid urbanization and recurrent droughts, threatening the resilience of these agroecosystems. These findings underscore the urgent need for concrete sustainable management policies for fruit trees particularly almonds to preserve this valuable native diversity. Recommended measures include ex situ conservation in gene banks, participatory selection, and in situ agroecological zoning. Furthermore, comprehensive analysis and the development of an in-situ conservation strategy are required. In the absence of such actions, this diversity risks being progressively replaced by uniform cultivars in the medium term and could disappear in the long term under drought stress, resulting in a significant loss of biodiversity at the national scale.