MacKenzie was largely a fringe player during his two seasons at Glanford Park, but found himself in the first-team regularly as the team won the League One title this season.
But despite impressing he was deemed surplus to requirements at the Iron, and moved to County on a free transfer.
He has signed a two-year deal at Meadow Lane, after being courted by several League Two clubs.
"The potential of the club was an important factor, they've had a tough few years but the potential to do well is there," he said.
"I'm sure the manager can get a few more good signings in, if we get things right on the pitch the club is geared to go on to a higher level.
"It is a big club to be joining, I'm glad it is out of the way and that I can look forward to the season. I feel there are exciting times ahead."