As a full-time starter in 2006, Jenkins earned All-Big Ten first team honors. He had his first career interception against Cincinnati on Sept. 16, and a week later scored his first career touchdown (a 61-yard interception return against Penn State). Malcolm Jenkins finished the season with four interceptions, seconnd on the team and first among Ohio State defensive backs.
Jenkins repeated as an All-Big Ten first-team selection in 2007, finishing with a team-high four interceptions and another touchdown. He had 47 total tackles and was a semifinalist for the Thorpe Award. He capped off his season with an interception in Ohio State's BCS National Championship Game loss against LSU.
In January of 2008, Malcolm Jenkins decided to return to Ohio State for his senior season, despite being one of the top cornerback prospects for the NFL Draft. He set goals to win the Thorpe Award, the national championship and be a first-team All-American. He accomplished both of his individual goals, finishing the season with 57 tackles and three interceptions. He beat out Eric Berry and Taylor Mays for the Jim Thorpe Award, given annually to the nation's best defensive back. However, Ohio State lost twice and settled for a berth in the Fiesta Bowl, after back-to-back appearances in the BCS National Championship Game. Jenkins had a team-high 10 tackles in Ohio State's 35-3 loss to USC, setting a new career high. He had four tackles in the 13-6 loss to Penn State.
After spending much of his rookie season buried on the depth chart, Jenkins earned his first career start in Week 11 against the Buccaneers. He recorded a seven tackles and had his first career interception. Jenkins finished the 2009 regular season with 55 total tackles and one interception in 14 games.
Jenkins played sparingly in the Saints first playoff game of 2009 and was inactive for the 2009 NFC Championship game win against the Minnesota Vikings. In Super Bowl XLIV, Jenkins recorded four total tackles and broke up a pass in the fourth quarter, helping the Saints win their first championship.