Fort Queenscliff Museum has a number of exhibits that are of special value. The collection includes:

• The documents relating to the 1860 occupation of Shortland Bluff and Captain Jordan
• The uniform of Lieutenant Colonel J.E. Newland, VC
• An Artillery bottle, from the soft drink factory inside the Fort
• The collection of items relating to Major Hany Ronald, perhaps the person with the longest association with the Fort
• The Major General W.A. Coxen CB, CMG, DSO collection
• The Roll Book of the Victorian Permanent Artillery from 1882 to 1905
• The rifle issued to the soldier murdered in Crow's Nest in 1942

The Museum also has a rare manual entitled "The Artillerist's Manual". The contents include Cautionary Remarks (on the importance of drill and bearing), Recruit (a section on basic foot drill), Manual and Platoon Exercises (more foot drill), Company Drill, Inspection on Review, Battalion Drill, Sword Exercise, Light Drill, Instruction in Gunnery and finally Cavalry Exercise. This manual may be the second or third oldest Australian Military Publication.