The Museum of the Center consists of a Natural History Museum (a 20 x 40 foot room), a Pollution/Recycling Museum ( a 30 x 50 foot room), and a 20 x 25 foot student microscope laboratory. Depending upon the grade level of the students, these various museums are in constant use throughout the school year.

The Natural History Museum houses a mineralogical display, fossil display, posters about the different types of Northwest Florida habitats, and various creatures (mainly snakes). Students are brought to this room to discuss the roles of these habitats, snakes, and other creatures in the natural world, Lucy the screeh owl is also displayed to the students.

The mineral display was constructed by one of the Center's partners, the Panhandle Gem and Mineralogical Society. The display exhibits the formation of different types of rocks and mineral structures including minerals which are used in everday life products. The "Society" also provides each student that visits the Center a sample rock or mineral. There are in excess of 27 different types of rocks and minerals provided to students. They range from Mica, collected in Alabama, to Amethyst collected in Brazil. The Society has given away over 100,000 samples of rocks and minerals to students.