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Maintaining agricultural diversity is important for the conservation of rare species and for preserving underlying ecosystem processes on which smallholder farmers rely. The positive effects of crop diversity are well documented in tropical systems, but the conservation potential of arid agricultural systems is less clear. This study assesses the impact of three arid agroforestry systems on plant diversity and functional richness in South Sinai, Egypt: (1) mountain orchard gardens, (2) modern town gardens and (3) low desert date-palm gardens. We surveyed plants (cultivated and wild) within gardens and control plots of natural habitat and allocated each plant eight biological traits that are recognised as being linked with major ecosystem processes. Species diversity was quantified using three measures (Hill’s numbers) and total species diversity was significantly higher within gardens than in the surrounding habitat at all three levels of diversity and across the three agroforestry systems. Species similarity was high between gardens and the surrounding habitat, and there was a strong overlap in the functional traits of wild plants and cultivated non-tree species. Despite the clear presence of trees within the gardens, the community weighted trait means (CWMs) showed that chamaephyte perennials were the dominant life-forms in both the gardens and the natural habitat. Functional richness differed between the three agroforestry systems, but was significantly higher within the gardens. Functional richness has been linked to increased productivity and CWMs showed that plants within the gardens were considerably taller than outside, suggesting higher biomass accumulation. These findings suggest that Bedouin agricultural practices are not having a negative effect on the flora of the region and that the continuation of these indigenous farming practices can actively benefit rare wild plants in the region. On a wider scale, this study supports the view that smallholder farms and homegardens can be valuable tools in conservation, preserving local species and maintaining ecosystem functioning.