Fruit intake in eastern Africa remains significantly below the recommended daily minimum, despite the vital role indigenous fruit trees play in enhancing nutrition and food security, particularly for vulnerable groups such as women and children. These trees offer a year-round source of micronutrient-rich products, yet their presence in natural vegetation is diminishing across the region, including in Sudan’s Nuba Mountains. Homegardens may present a viable solution for conserving and cultivating indigenous fruit trees, but data on their diversity within such systems is limited. This study assessed plant diversity in 17 randomly selected homegardens in a Nuba village, evaluating both species composition and influencing environmental and socioeconomic factors. A total of 103 plant species were identified, comprising 40 tree and shrub species, with an average of 22 species per garden. Fruit species represented 15% of total species but only 0.04% of all plant individuals, due to the prevalence of annual vegetables. Indigenous fruit tree diversity was low, with only 12 species found across gardens, averaging 2.5 species per garden and a Shannon index of 0.8. Garden size was positively correlated with species richness (R²=0.315) but negatively with Shannon evenness (R²=0.352), while other variables such as gardener age, gender, commercialization, and ethnicity showed no significant influence. Notably, none of the indigenous fruit trees had been deliberately planted; instead, they were preserved during land clearance, often valued more for fencing, fodder, or fiber than for fruit. Enhancing indigenous fruit tree use requires access to quality planting material and improved cultivation knowledge among local gardeners.