As a result of increasing global demand for food, large areas of natural habitat are being converted to agroecosystems to accommodate crop cultivation. This agricultural expansion is most prominent in the tropics, where many rural communities are dependent solely on farming income for their livelihoods. Such agricultural land conversion can have severe implications for local fauna. In this study, we compared vertebrate species diversity between natural forest habitat and three types of vanilla plantations maintained under varying management regimes in north-east Madagascar. We used diurnal and nocturnal transects to survey vertebrate diversity. Natural forest habitat contained the greatest vertebrate species diversity, and had proportionally more threatened and endemic species than all vanilla plantation types. However, we observed a greater number of species and a higher inverse Simpson index in minimally managed vanilla plantations located within or near natural forest compared to intensively managed vanilla plantations. These findings are important and encouraging for animal conservation and sustainable crop cultivation in Madagascar, and suggest that newly created vanilla plantations, and already existing plantations, should endeavour to follow the more traditional, minimalistic management approach to improve sustainability and promote higher faunal diversity.