Much of the museum's lower level is devoted to the Society's military collection. It includes memorabilia and artifacts associated with military conflicts throughout the years from the Blackhawk War that took place in Stephenson County to the Gulf War.

This room is devoted to Civil War items, many of which are from the 46th Illinois Infantry. The 46th had more Freeport boys than any other Civil War unit and earned the nickname, "The Freeport Boys."

Among the unique items in the Civil War collection is this amputation kit used by Civil War surgeons.