The Eagles scored the game's first 10 points before second-half miscues sealed their fate in a 35-10 loss at Williams Stadium. Liberty is ranked No. 24 in the Division I FCS coaches' poll.
NCCU fell to 0-2 after a pair of road games while the Flames - who fell 33-20 at West Virginia in their opener - evened their record at 1-1.
The Eagles took advantage of a short field twice early in the game.
A fumble recovery at the Flames' 21 set up Michael Johnson's six-yard scoring toss to Will Scott late in the first quarter, and a short punt that allowed the Eagles to take over at the hosts' 36 set up a 35-yard field goal from Frankie Cardelle for the 10-0 lead.
But after that it was all Liberty.
The biggest turning point in the game came with 10:05 left in the game with the Flames up 14-10. Johnson (pictured) was sacked at his own 1-yard line and lost a fumble, setting up the first of three fourth-quarter touchdowns the Flames used to put the game away.
Liberty finished with 328 yards total offense - 231 of that on the ground - to 213 for the Eagles that included just 43 yards rushing.
Johnson completed 17 of 22 passes for 121 yards for the touchdown and one interception, while Tim Shankle rushed 26 times for 81 yards.
The Eagles will play their home opener on Sept. 19 at 1:30 against Morehead State of the non-scholarship Pioneer Football League.