West African flood-plains have undergone major land-use transformations in the second half of the 20th century. To obtain insight in the effect of flood-plain development for irrigated rice cultivation on the abundance, richness, and diversity of Palearctic and Afrotropical raptors, we conducted monthly transect surveys covering dry and wet seasons in four major habitats on the Waza-Logone flood-plain of Cameroon: dry grasslands, cultivated grasslands, rice fields, and seasonally flooded grasslands resembling natural flood-plain vegetation. We recorded 36 raptor species among 2,533 individuals, dominated by Black Kite Milvus migrans, which comprised 42% of counts. Although richness and diversity were not related to land-use for Palearctic raptors, Afrotropical raptor diversity was higher on the flooded grasslands compared to the newly created cultivated habitats and dry grasslands. The abundance of Afrotropical raptors did not significantly differ across habitats but was lower in rice-fields when Black Kite and Hooded Vulture Necrosyrtes monachus were excluded. Conversely, Palearctic raptor abundance was highest in post-harvest rice fields, demonstrating the importance of the rice fields as foraging habitat for Palearctic raptors. Further transformation of West Africa’s flood-plains is expected, reducing their capacity for Afrotropical raptors, while Palearctic raptors may benefit from expansion of rice-fields, but more research is needed on their vulnerability to pesticide use.