Holmes suffered from soreness in his leg after collapsing in a match against Rushden & Diamonds in December 2001. He returned to action to score from the edge of the penalty area in a 3–1 away victory against Swansea City on 30 March 2002; this goal secured Luton's promotion to the Second Division at the first attempt. Holmes' 2001–02 season was ended with 10 appearances and one goal after suffering a knee ligament injury during Luton's 4–0 victory at Hull City on 6 April 2002. He suffered a groin strain during the 2–1 home defeat to Cambridge United in the Football League Trophy on 10 December 2002. He made his return to Luton's first team in a 3–2 away defeat to Mansfield Town on 4 March 2003 after coming on as a 74th-minute substitute. He then scored in the following match against Huddersfield Town, being assisted by an Ian Hillier cross in the 71st minute to help Luton to a 3–0 victory on 8 March 2003. He finished 2002–03 with 23 appearances and two goals, but missed Luton's final match of the season after picking up a hamstring injury during a 1–1 draw with Stockport County on 26 April 2003.