The Museum of Ouidah 's permanent collections depict the history and traditions of the region's inhabitants. Beginning with artifacts from the old Portuguese Fort (in which the Museum of Ouidah is housed), the collections proceed to describe through objects, imagery, and artifacts the history of the kingdom of Xwéda and kingdom of Dahomey, both of which were dependent on the trade in enslaved individuals with Europeans for riches and power. Photos and artifacts portray the impact that people from Benin made on the cultures of New World societies, as well as the effects of mass repatriation to Benin after the decline of the slave trade. Finally, local religious tradition is characterized through many current religious items and photos from local ceremonies.

In addition to the museum's permanent collection, starting June 11, 2006 the museum will host “The Lost Communities of the Xwéda Kingdom ” exhibit. This exhibit will expand on the museum's permanent holdings through illustration of the life in the Xwédan countryside.