He was released by Rotherham at the end of the season, after not being offered a new contract by the club, and he was signed by Conference North club Harrogate Town on 25 September 2009. Holmes made his first and only appearance for Harrogate in a 4–0 away defeat to Bradford Park Avenue in the FA Cup second qualifying round on 26 September 2009. He joined Conference Premier club Ebbsfleet United on 9 October 2009, making his debut a day later in a 4–0 defeat to Cambridge United. His first goal was with the winner in a 2–1 victory over Mansfield Town on 28 November 2009, scoring from close range from a Magno Vieira pass. He made 29 appearances and scored two goals for Ebbsfleet during the 2009–10 as they were relegated to the Conference South.