Baynes was aboard "Asia", the British flagship during the Battle of Navarino on 20 October 1827 during the Greek War of Independence from the Ottoman Empire. A joint British-French-Russian fleet attacked a larger, joint Ottoman-Egyptian fleet in Navarino Bay. "Asia" led the line of battle and the steady fire by the British-French-Russian fleet led to their victory. Baynes distinguished himself during the battle and was promoted to captain on 8 July 1828. He was also made a companion of the Bath, a knight in the Greek Order of the Redeemer and received two other honours.