After leaving the Ayrshire Combination, the club struggled to find an alternative league in which to play. In 1900-01, the club played in the North Ayrshire League, finishing second behind Beith F.C., but the competition only had 7 clubs, and the club withdrew from the competition the next season. In 1903-04 the club was one of the six founder members of the Ayrshire & Renfrewshire League, finishing third, but Annbank did not play in the league's second and final season.
