His next post was as Governor for the Lagos Colony where he negotiated treaties with the local chiefs which protected Christian missionaries and ending human sacrifies.

[2] Carter became the private secretary to Sir George Berkeley, Governor of the Leeward Islands, in 1875.

[12] Carter (from his official residence in Bathurst) sent an envoy with a message that if the abuses continued, "he might expect a visit of a disciplinary nature from the marine forces of the Queen of England [sic].

[14] Carter travelled to various parts of Yorubaland, accompanied by soldiers, in an attempt to demonstrate the might of the British.

[14] Carter was not well received at Oyo, and the Egba chiefs advised him not to interfere with slavery, while the Ibadan chiefs said they were afraid that their slaves would "assert their freedom by running to the Resident" – and they refused to sign a treaty with Carter that would impose a Resident on the city.

[15] It was agreed that freedom of trade between the Egba Nation and Lagos was to be guaranteed by the British Government,[16] in return for which no road would be closed without the approval of the Governor.

[15] He was promoted Knight Commander of the Order of St Michael and St George (KCMG) on 3 June 1893,[17] "in recognition of his services in conducting a mission to the Yoruba country which resulted in the negotiation of important treaties and brought to an end a long-standing war.

[24] She became his second wife on 25 August 1903, when they were married in the Church of the Advent in Boston and had a son, John Codman Carter.

[22][24] Carter continued working in senior colonial positions — being appointed the Governor and Commander-in-Chief of the Island of Barbados and its Dependencies[21] in 1904, and as Administrator of the Government of the Colony of Trinidad and Tobago, and its Dependencies in the absence of the Governor from 1907 until 1910,[25] whereupon he retired.

[3] In the early 1920s, he moved back to Barbados, and lived at Ilaro Court, which had been designed and built by Lady Gilbert Carter.