Although the "Conqueror's" sails and rigging suffered considerable damage, she suffered only three dead and nine wounded despite being in the thick of battle, and returned to Gibraltar largely unharmed by the large storm which followed the action, and was even able to help some more crippled ships back to port. After Trafalgar the "Conqueror" helped continue to blockade Cádiz and then, in 1807, was in the squadron sent to secure the Portuguese fleet and royal family. She remained off the Portuguese coast during much of 1808, eventually returning home after the surrender of Siniavin's Russian squadron in the Tagus. Pellew then left her and was appointed to superintend the payment of ships in the Medway.