He joined Dundee on a free transfer in June 2006 under the management of Alex Rae and signed a two-year contract.

[7] However, several days later, in the quarter final of Scottish League Cup, MacKenzie scored an own-goal against his former club, Rangers.

On 30 October 2010, MacKenzie received a straight red card after a professional foul, as MK Dons lost 4–2 against Tranmere Rovers.

On 17 September 2011, he made assist Dean Lewington before being sent-off for stamping on Alan Lee, in a 1–1 draw against Huddersfield Town.

After the match, Robinson was disappointed with his action, though he was sarcastically proud of him "in a weird way for coming out and accepting his punishment.

The day after signing for the club, MacKenzie made his debut in a goalless draw with Bristol City.

MacKenzie joined Scottish Championship side St Mirren in June 2016, signing a one-year contract with the club.

[29] After establishing himself as a first team regular and scoring 5 goals, MacKenzie agreed a one-year contract extension with the club in May 2017.

[30] Despite suffering from injuries MacKenzie was able to play 18 times for Saints and helped them lift the 2017–18 Scottish Championship title, which lead to him signing a further one-year contract extension in May 2018.

[31] Injury once again led to MacKenzie missing a large part of the following season, after he had to undergo surgery in August 2018.