He served as part of the Tangier Garrison, something he had in common with other leading figures of the Siege of Derry such as Robert Lundy, Percy Kirke and John Mitchelburne.
Following the Irish Protestant rebellion against James II in 1688–89, Baker joined a newly raised regiment in Eastern Ulster.
He was present during a failed attack on Carrickfergus and then at the Break of Dromore when an Irish Army force under Richard Hamilton routed Arthur Rawdon's Protestant troops.
After the previous Governor Robert Lundy had resigned his post and left the city, Baker was offered the governorship.
After he fell ill command was handed over to John Mitchelburne, who was formally elected governor after Baker's death.