Despite the emerging and promising of on-farm trees to the biodiversity conservation, economic and ecological importance, there is still a dearth of empirical scientific information on how farmers manage trees to improve floristic diversity across Agroforestry land uses in semi-arid. Therefore, this research was aimed to (i) investigate and compare the floristic composition and diversity across three Agroforestry practices; (ii) examine regeneration status of selected trees species; (iii) describe management practices and species preference. Two peasant associations (Anabelesa and Digba) were purposively selected. Then, farmers who practice homegardens, parklands, live fencings and woodlots were stratified based on local wealth category. “91” households were randomly selected from each wealth category. Different quadrats were laid out for inventory. 24 key informants were used. The data was analyzed using SPSS version 20.0 software. A total of 49 woody species, belonging to 44 genera and 30 families were encountered across the four land uses. The mean Shannon diversity index of rich farmers was higher over medium and poor. The mean basal area and stem number ranged from 0.27 to 48.2 m² ha⁻¹ and 9.48 to 2320.83 stems ha⁻¹, respectively. Trees with the top five highest IVI in homegardens and live fencings was showed a Reversed J-shaped diameter class distribution. Farmers employed pruning, thinning, composting, pollarding, lopping, coppicing, weeding, protection and watering. Species Preference was influenced by the purposes of trees. These results suggest that acknowledging the farmers’ indigenous knowledge on trees management is crucial for enhancing biodiversity conservation in the agricultural ecosystems in semi-arid.