Baker was appointed a lieutenant by George Legge, 1st Baron Dartmouth on 14 November 1688; on 12 October 1691 he was advanced to be captain of , and during the Nine Years' War with France successively commanded , , , and , for the greater part of the time in the Mediterranean, but without any opportunity of especial distinction. Early in 1701, during the War of the Spanish Succession he was appointed to , and a year later to the 66-gun , in which he continued for nearly six years, serving in the grand fleet under Sir George Rooke or Sir Cloudesley Shovell, at the Battles of Cadiz and Vigo Bay in 1702, at the Capture of Gibraltar and the Battle of Málaga in 1704, at the Siege of Barcelona in 1705, and the Battle of Toulon in 1707.