After the peace of Amiens, Lowe, now a Major, became assistant quartermaster-general. On the renewal of war with France in 1803, he was charged, as a lieutenant-colonel, to raise the Corsican battalion again and with it assisted in the defense of Sicily. On the capture of Capri, he proceeded there with his battalion and a Maltese regiment; but in October 1808, Joachim Murat ordered an attack upon the island, which was organized by General Lamarque. Lowe, owing to the unreliability of the Maltese troops and no hope of help by sea, had to agree to evacuate the island. Sir William Napier criticized him, but his garrison consisted of only 1362 men, while the assailants numbered between 3000 and 4000.