The current collections of the Carlos Machado Museum, subject to minor collections in the field of epigraphy, agro-industrial and decorative arts technologies, spread across four main sections: Natural History, Art, Religious Art and Ethnography.

The Natural History collections relate to the museum’s founding in the late nineteenth century, and reflect the scientific spirit of the age. They include examples of different parts of the globe, although predominate Azorean specimens. There are remarkable collections of fish, crustaceans, birds, mammals, mollusks, insects, arachnids, reptiles, flora, geology and mineralogy. Much of the collection also features the original founder of the labels.