As natural forests contract, farming systems become increasingly important to landscape biodiversity conservation, yet assets and limits of their contribution are insufficiently documented. A sound understanding of farmer strategies in the management of on-farm tree biodiversity is also critical to landscape approaches for biodiversity conservation and livelihood improvement. Diversity and management of woody species were surveyed in 105 farms around Mabira Forest in South-Central Uganda. Farms were selected according to distance to forest, landscape axis, gender, wealth, and specialized forest use of household heads. Farmer management has a strong influence on tree diversity in the coffee–banana systems around Mabira Forest. This is reflected in the relatively high number of planted and exotic species at the levels of farm niche, farm and landscape. Both the number of years under cultivation and farmer involvement in specialized forest use were conducive to higher species diversity. Gender, wealth and tenure status did not influence tree diversity. Variation in on-farm species richness was noted between landscape axes radiating out of the forest rather than concentric distance categories. Farming systems around Mabira Forest Reserve provide a key complementary rather than substitute tree diversity refuge and can be managed to enhance overall landscape biodiversity.