The NCAA has been investigating the recruitment of signee Jovon Robinson, who was ruled ineligible after a guidance counselor admitted to creating a fake transcript.
"I feel very confident that everything is fine, and that's my understanding," Malzahn said.
The Tigers badly struggled in a transition to Scot Loeffler's pro-style last season, starting three quarterbacks.
Auburn was ranked in the top seven in rushing, total and scoring offense in 2010 and Newton won the Heisman Trophy in his lone season out of the junior college ranks. It was the Tigers' first national title since 1957.
Without Newton, the Tigers slipped to 100th in total offense in 2011 and then dipped even further.
The defense struggled, too. Defensive end Nosa Eguae said he thinks Malzahn was the right guy.
"I know coach Malzahn, and he's an amazing man," Eguae said. "He's a standup guy. I'm looking forward to the future. I can't wait to get started and turn this thing around and get some wins."
The hiring reunites Malzahn with the quarterback he recruited out of Arkansas. Kiehl Frazier was benched last season after struggling as the starter. He was USA Today's national offensive player of the year as a high school senior.
Malzahn had been earning $1.3 million a year for the Tigers after interviewing with Vanderbilt after the national championship season. He took a substantial pay cut to join the head coaching ranks with the Sun Belt Conference team. Malzahn replaced Hugh Freeze, who also left after one season at Arkansas State to take over at Mississippi.
Chizik's tenure was marred by off-the-field problems, including the arrest of four players from the championship team for armed robbery.
Malzahn also made a couple of decisions with players that didn't pan out. Tailback Mike Dyer transferred from Auburn — where he was suspended — to Arkansas State. He was then dismissed by Arkansas State in July after a state trooper found marijuana and a gun in a car the national title game MVP was driving.
Jacobs said discipline was a factor in choosing Malzahn.
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