MPM's Geology collections had their origin in the materials gathered in the 1850s by Peter Engelmann for educational use at the newly established German-English Academy.

In 1879, the collections were incorporated into the Natural History Society of Wisconsin (the foundation for the Milwaukee Public Museum) and included 3500 rocks and minerals, and 1870 fossils.

Today, the department has extensive collections of Lower Paleozoic (Cambrian, Ordovician, Silurian) fossils from Wisconsin and adjacent states plus sizable collections from the Great Basin, the eastern United States, and parts of Europe. There are small collections of invertebrate fossils from other time intervals and regions (totaling about 43,000 specimens), an eclectic collection of Pleistocene vertebrate specimens from the Midwest and small collections of Late Cretaceous vertebrates from the Hell Creek Formation of Montana and North Dakota (about 50,000 specimens combined). There are also small collections of about 600 type specimens, more than 23,000 plant fossils, some 35,000 rocks and minerals, and meteorites.