In January 2012, Mark was loaned out to Scottish Premier League club Aberdeen. On moving to Aberdeen, Reynolds once again joined up with manager Craig Brown, who had previously been his manager at Motherwell. Reynolds who was brought in as a replacement for Richard Foster, made his debut in a 0–0 draw against Kilmarnock on 14 January 2012. In March, Reynolds played twice against his former club (one in the SFA Cup and other in the League). On 2 May 2012, Reynolds scored an own goal early on in a game with Hibernian at Pittodrie, in which the visitors went on to win 2–1.
After being told by Sheffield Wednesday manager Dave Jones that he was surplus to requirements and won’t get first team guarantee, Reynolds returned to Aberdeen on loan for the 2012–13 season. Upon joining Aberdeen for the second time, Reynolds says he joined the club instead of Rangers, quoting: “It was brought to my attention that Rangers were interested but it’s a strange situation there at the moment. If you go there you’re almost writing off three years of your career to go play in the Third Division. But as a player you’ve got to sacrifice three years before you’re back there playing in the SPL again.”
He played his first match of his second loan spell, coming on as a substitute, in a 2–1 win over St Johnstone on 18 August 2012 and two months later, he scored his first goal in a 4–1 win over St Mirren. The following month, Aberdeen chief executive Duncan Fraser announced that the club had opened negotiations to sign Reynolds on a permanent deal, with a possible three-year contract on the table. Shortly after being released from Sheffield Wednesday, Reynolds rejoined Aberdeen on a free transfer, signing a four-and-a-half-year contract.
Reynolds was appointed vice-captain of Aberdeen for the 2013–14 season. He scored his first goal for the club, in a 3–1 win against his former club, Motherwell and then scored his another of the season on 5 January 2014, in a 1–0 win over Kilmarnock. On 28 February 2014, Reynolds signed a new four-year contract extension. At that time former Aberdeen captain Willie Miller compared Reynolds’s central defensive partnership with Russell Anderson to his own successful pairing with Alex McLeish.
The following month, Reynolds made history as he started in the 2014 Scottish League Cup Final victory against Inverness Caledonian Thistle, making it his first domestic honour and Aberdeen’s first piece of silverware in 19 years.
In 2014–15 season, Reynolds featured in six matches in the Europa League and scored his first European goal in the second leg of third round, as Aberdeen lost 3–2 to Real Sociedad.