Agricultural production in northern Benin is characterized by smallholder traditional agroforestry systems, with on-farm remnant tree species. Among its numerous advantages, agroforestry is known for its valuable contribution to biodiversity conservation. This study quantifies the importance of Vitellaria paradoxa C.F. Gaertn agroforests in terms of woody species conservation in Atacora district in Benin. Forest inventories were performed within 50×50 m plots constructed on a net grid map of Atacora district. Diversity indices were computed for both adult and juvenile species in two land management regimes: fields and fallows. Overall 41 woody species were recorded; 28 in fields and 36 in fallows. Taking into account matured and juvenile individuals, the diversity of woody species increased: 86 species in total; 69 species in fields and 78 in fallows. The biodiversity of V. paradoxa’s agroforestry parklands increases from fields to fallows, and decreases from bulk species (considering mature and juvenile speies) to adult ones. Leguminosae and Combretaceae were the most abundant families registered. From the Cover Value Index, V. paradoxa, Parkia biglobosa, Lannea microcarpa, Lannea acida and Diospiros mespiliformis were the most abundant species. Support for maintaining this kind of agricultural system is needed, as this exemplifies the synergy for providing, provisioning and supporting services and biodiversity conservation.