The National Museum of Naval Aviation, on station, is exactly what it says, and includes a great many navy planes, historic equipment, and exhibits on topics back to the start of naval aviation, much of which was at NAS Pensacola itself (originally Warrington Naval Yard). The museum has an education program, including offboard outreach and onboard summer camps. Visitors can see Navy propellor planes from World War II flattops, simulate a Blue Angel flight, "fly" a cockpit trainer, and view various items from different eras on display with explanations.

The Pensacola Museum of Art, in the former Pensacola jail, features modern, contemporary, and some decorative arts.

Historic Pensacola Village is a University of Western Florida effort to preserve local heritage, and includes several buildings downtown, including some historic reenactment and living history locations, and a great many preserved houses and business from various historic periods. The same organization operates the Historic Pensacola Museum of Industry and Historic Pensacola Museum of Commerce.

The Pensacola Lighthouse is an old facility going back to before the Civil War, and still in use today. This tower was an object of contention during the Civil War and has warned of sea hazards for over 150 years.

The Civil War Soldier's Museum is a small museum dedicated to presenting the lives of the men who fought the Civil War, and includes various displays and exhibits, including some actual items used in the period.

Fort Barrancas and Fort Pickens were US Army coastal defense batteries; Fort Barrancas is now on board NAS Pensacola; Fort Pickens is across the mouth of Pensacola Bay, on Santa Rosa Island. There are interpretive signs and preserved fortifications. The other major fort once also defending the port of Pensacola, Fort McRee, has withered away.

The T.T. Wentworth, Jr. Florida State Museum started as a collection of strange random items, but gradually became a collection of Florida and especially Panhandle Florida historic items. The old curiosities are still on display on the first floor; the rest of the museum has other historic items.

The Florida Public Archeology Network is not a museum itself, but is a public effort to investigate, recover, and preserve native and settler ruins and items for study and display.