Nowadays, the conservation of biodiversity is a major environmental challenge globally. Homegarden agroforestry systems (HGAFs) have a large potential for biodiversity conservation. However, little attention has been given to the relative importance of HGAFs in terms of biodiversity conservation. The present study, therefore, aimed to estimate and compare the woody species diversity and structure of HGAFs and adjacent natural forest (NF) in Northern Ethiopia. Three sites were purposively selected based on the presence of HGAFs and NF adjacent to each other. A stratified sampling system was used to select representative homegardens from different wealth categories. In NF, a systematic transect sampling technique was employed. A total of 90 sample plots (10 m × 20 m) were used to collect vegetation data. A total of 32 species representing 26 genera and 20 families were identified from the studied HGAFs and NF. Thirty woody species belonging to 24 genera and 20 families were recorded in the HGAFs whereas, 11 species, belonging to 9 genera and 8 families were recorded in the NF. Native woody species accounted for 66% of all woody species recorded in both HGAFs and NF. Stem density, richness, and diversities of woody species were significantly higher in HGAFs than in NF (p ≤ 0.05). Trees and shrubs in the HGAFs had significantly lower stem diameters, height, and basal area than the adjacent NF (p ≤ 0.05). The results show that HGAFs complements the NF for biodiversity conservation and supports in counteracting the loss of woody species from the natural ecosystem. Hence, promoting HGAFs habitats in human-dominated landscapes should be part of the biodiversity conservation strategy.