At the outbreak of the Napoleonic Wars, Brenton was given command of the frigate HMS "Minerve" but he was taken prisoner soon afterwards when his ship ran aground near Cherbourg. He spent three and a half years in captivity in France before he was exchanged for a French prisoner of war and was subsequently given command of HMS "Spartan". Brenton returned to the Mediterranean in 1807 where he launched a disastrous attack on an armed polacre which earned a strong rebuke from Vice Admiral Lord Collingwood. He salvaged his reputation undertaking a series of notable exploits while commanding a squadron of frigates in the Adriatic, and assisted with the capture several French Ionian Islands. In May 1810, he fought a successful action against a Neapolitan squadron near Naples in which he was severely wounded by enemy grapeshot. Brenton was rewarded with a baronetcy and a knighthood but his wound troubled him for the rest of his life.