After the war, Baker co-ordinated administrative services in the Allied Control Commission in Germany. Promoted to the substantive rank of major on 1 July 1946, he was appointed Deputy Director of Staff Duties at the War Office in January 1947. After promotion to lieutenant colonel on 31 December 1951, he took command of 3rd Regiment Royal Horse Artillery at Munsterlager and, following promotion to colonel on 20 June 1953 and having been appointed a Companion of the Order of the Bath in the New Year Honours 1955, he became Director of Operations and Chief of Staff for the campaign against EOKA in Cyprus in November 1955 during the Cyprus Emergency, for which he was appointed a Companion of the Order of St Michael and St George in the New Year Honours 1958. He became Assistant Chief of Staff at Headquarters Northern Army Group in February 1959 and, on promotion to major general on 3 February 1960, he was appointed Chief-of-Staff at Southern Command. He went on to be Chief of Staff at Supreme Headquarters Allied Powers Europe (SHAPE) in November 1961, in which capacity he was responsible for contingency planning for Berlin at the time of the construction of the Berlin Wall.