When war broke out in October 1899, and British troops stood to conquer Bloemfontein in March 1900, Blignaut organised the removal of the government to Kroonstad, including the state archives. Afterwards he stayed with the government in the field, moving from place to place. In January 1901, gravely ill, he was issued with a laissez-passer to travel to his farm Secretarispan near Bloemfontein, where he stayed for the remainder of the war, effectively on leave from his position as Government Secretary.