In 1807 the French and British were again at war with each other and extending that conflict around the world. The United States was a neutral party in the conflict offering supplies and repairs to the navies of both nations. Just prior to June of 1807, two French frigates limped into the harbor of Norfok having suffered damage in a storm. Both ships were placed in the Gosport Navy yard at Portsmouth, Virginia. The British admiralty upon hearing of the location of the French ships ordered the HMS Leopard (50 guns) to proceed to the Virginia coast and attempt to engage and destroy the French ships upon their departure. Several smaller ships accompanied the Leopard.

During this period the USS Chesapeake (38 guns) was preparing for a deployment to the Mediterreanian Sea to become the flag ship there under Commodore James Barron. As the Chesapeake was leaving the bay, the HMS Leopard hailed her and Commodore Barron, extending Naval courtesy, stopped his ship and allowed the British to come on board. The commodore was presented with a request to muster the crew for inspection by the British officers in order to recover British deserters. Commodore Barron refused stating he had no dersters in his crew. Upon the return of the officers to the HMS Leopard, the Leopard immediately unleashed a broad side into the unsuspecting Chesapeake. Being totally unprepared for this attack, the Chesapeake suffered severely under three additional broad sides before having to stike her colors. The British then returned and removed four crew members and only one turned out to be a deserter from the British service.

Upon the return of the Chesapeake to Norfolk, the citizens there decided to place restrictions on the trade with British warships in retaliation for the attack on the Chesapeake. Two weeks later, Thomas Matthews wrote to the governor of Virginia that through the efforts of the people of Norfolk, Fort Norfolk had been repaired and has nine eighteen pounder guns mounted for the defense of the city. War was averted for a time through negotiations and the efforts of then President Jefferson.

In 1808 Captain Wlker Keith Armistead was assigned as the Superintending Engineer of the Norfolk area defenses. Captain Armistead then proceeded to rebuild the forts in the area and bring them in line with the Second System of Seacoast Fortifications. This involved building masonry outer walls that were backed by earth with gun and musket platforms for defense of the fort. Fort Norfolk was designed to originally mount 30 cannon of various weights. The largest, 18 and 24 pounders, were for the river side to repel warships while the smaller garrison guns were for defense against land attacks. Two brick barracks were built for two companies of men and officers at seperate ends of the fort. A brick magazine to house 100 barrels of powder was also built near the rear of the fort. The fort also had a hot shot furnance to facilitate the heating of cannon balls to be fired into attacking ships. Fort Norfolk was maintained for the next two years by a company of regular artillery and one of regular infantry.