During his junior season in 2003, Martin started the first four games of the season before new head coach Ron Zook replaced him in the starting lineup with Chris Leak, one of the nation's top freshmen quarterback recruits, after Martin suffered a concussion against the Miami Hurricanes. After replacing Ingle in the fourth game of the season, Leak remained the starter for the rest of the year, placing Martin's quarterback career as a Gator in limbo. In Martin's four starts against San Jose State Spartans, Miami Hurricanes, Florida A&M Rattlers and Tennessee Volunteers, he completed forty-seven of seventy-seven passes (a 61.0% completion average) for 654 yards and three touchdowns, and a quarterback efficiency rating of 140.5.