The 27-year-old defender, who made 12 appearances for the Seasiders during a loan spell last season, has signed a two-year deal with an option for a further year.
"It's good to have it all tied up now and be able to focus on the new season," said MacKenzie.
"I'm just looking forward to getting out on the training pitch with the boys again and planning for the start of the season.
"I enjoyed my time here last season and the three months that I had here were pretty good. It gave me a wee taste of Championship football and it kind of made my mind up of where I wanted to try and play.
"I've been given the opportunity to come here and do that so hopefully I can do well."
MacKenzie joined MK Dons from Dundee in 2010 and made 79 appearances during his three years at the club.
Injuries and suspensions prevented the Scot from reaching a century of appearances for the Dons but he was still a key player in two play-off campaigns.
Dons boss Karl Robinson said: "Gary has been a tremendous servant to this football club and has matured both on and off the pitch during his time in Milton Keynes.
"It is not in this club's nature to stand in the way of a player's own personal progression and the opportunity to play in the Championship, and perhaps get the Scotland cap that currently eludes him, is too good to turn down."