Conspicuous trees and other perennial plants in smallholders’ farms have been acknowledged for their biodiversity conservation values. Impacts of agroforestry practices, elevation gradients, wealth status on perennial plant composition, diversity, and structure were empirically assessed. Four agroforestry practices were considered, namely, dispersed trees in perennial crops, homesteads, boundary plantations, and woodlots. In all, 540 sample plots were randomly selected and surveyed. A total of 138 perennial plant species belongs to 113 genera and 62 families were identified and recorded. Of the species, 79% were trees, 18% shrubs, and 3% non-woody perennials. Also, 83% of identified plant species were native. A substantial proportion of the species (71%) were naturally regenerated. The highest native woody plant species were found in homesteads (75%) and the least in woodlots (15%). Dimensionality in species compositions across agroforestry practices was graphically displayed using none-metric multidimensional scaling and there were significant differences (p < 0.001). Species richness was significantly highest in homesteads (72.3 ± 3.5), while Shannon diversity (2.5 ± 0.2) in boundary plantation (p < 0.001). Middle altitude and rich households had harbored significantly the highest species richness, Shannon diversity index, and Simpson evenness index (p < 0.05). The general linear model showed the primary interactions of determinants had significantly positive effects on biodiversity values (p < 0.001). The study reveals agroforestry interventions should consider agroforestry practices, socioeconomic settings, elevation gradients, and interactions among them in favoring or disfavoring the growing of native perennial plant species on the agricultural landscape in the central highland of Ethiopia and beyond in the tropics.