Cotton eventually rose to be Chief Commissioner of Assam (1896 to 1902), during which time he experienced the 1897 Assam earthquake. The Viceroy, Lord Curzon, visited Assam in March 1900, and in an address afterwards praised Cotton's "″effort and interest in the province″", but was otherways unusually careful not to promise much in his speeches during the visit. Cotton College, Guwahati was established in 1901 by Cotton. As he retired, he was appointed a Knight Commander of the Order of the Star of India (KCSI) in the 1902 Coronation Honours list published on 26 June 1902, and invested as such by King Edward VII at Buckingham Palace on 24 October 1902.