On 5 June 2013, it was announced that MacDonald had signed with recently relegated SPL side Dundee with fellow former Morton full-back Willie Dyer. MacDonald scored his first goal for The Dees in a 5–0 win at Clyde in a pre-season friendly. On the first day of the SPFL Championship, "Peaso" put Dundee ahead against Queen of the South, but they lost the game 4–3 at Palmerston. He then netted twice at Dens in extra time to put Dundee past Forfar in the Ramsdens Cup, then put another past them in the League Cup, a free kick in the dying moments of extra time. The striker scored again when Livingston came to Dens, hit a penalty in against Stenhousemuir in the Ramsdens Cup, then another in a shootout. His next goals came against his former club Morton when he scored twice.
MacDonald was proving to be a key player as Dundee pushed for the top of the league, and scored four goals in three games, twice away to Dumbarton, once more against Queen of the South, then in a 2–1 defeat at Livingston where he also missed a penalty. When Dundee visited Hamilton hoping to reel in the team top of the league, "Peaso" struck with a diving header in the last few minutes after a shot from Martin Boyle had come off the bar to give the Dees a 3–0 win. He rounded off 2013 with a goal against Alloa then another two against Dumbarton. The 33-year-old had to wait until the 1st of March for his next goal in a 2–0 win against his former employers Morton, with new manager Paul Hartley now in charge. He scored again a fortnight later when The Dark Blues visited Livingston, a curling free kick to keep Dundee top of the league in a 2–0 victory.
MacDonald was released by Dundee in January 2015
1 How did you become a Dundee player?
I first spoke to bomber roundabout march time and I asked are you looking for a striker as a joke and he said yeah I will give you a call, he then had me scouted a few times and I had agreed a deal at the end of May
2 Do you wish you joined us sooner?
Yes 100%, I didn't realise how big a club Dundee where and how nice the people at the club where, I wish I had more than 18 months there and gutted I tore my cruciate against Celtic as I thought I was playing well at the time
3 Who were you closest to in time at Dundee?
It has to be Wullie dyer, I've looked after him since he was a kid at St Johnstone and also believe it or not I got him to Morton and also Dundee, as Allan Moore was needing a left back at the time so I recommended him and also bomber the same, so Wullie went on trial for a few days with Dundee and then signed along with me
4 Soapy says explain 'ayunpa' in 98?
Sun, sea, and lots and lots of drink ??
5 Best manager and captain to work with?
I've loved working under every manager I've had but I think for tactical and fine detail it has to be Derek McInnes and the best captain is Gav Rae as he worked behind the scenes for the lads like you wouldn't believe
6 Your best goal in a dee shirt?
I scored 2 free kicks vs Forfar a week after each other so either one of them but my most important goal I've ever scored was against Dumbarton to win the league, I can't explain the feeling but it was emotional as I had wanted to win so so much
7 Winning league back to 2 back which felt better Dundee/Morton?
Defo Dundee as I played every game except one but for Morton I arrived mid-January so I played a bit part in it but still was great to win it and notch a few more goals
8 What do you think of the group?
The group of lads in that dressing room where amazing, we recently had a reunion in Glasgow which Gav Rae was back from Oz for and I'm sure we will have many more as that was best dressing room I have been in .
9 What was it like to work with Jim Duffy?
Jim Duffy was brilliant, a great gaffer and a man’s man, he didn't bullshit and told you how it was which there ain't many gaffers like that about any-more, I loved playing under him and I'm not surprised how he has done at Morton with a very small budget in that league
10 How did the boys adjust to current gaffer after bomber left?
We just had to get on with it as that's football and managers come and go but usually not when you’re a point clear at top of the league and 20 seconds from being 4 clear, it was tough at first as Paul was told we were not fit so Tam Ritchie the fitness coach gave us a mini pre-season in March but then realised we were fit and stopped running us
11 You and Deefiant hero Higgy now play together at Clyde what's he like to play along with and have exchanged and DFC stories?
Higgy is a quality player and we have linked up well so far, we ain't spoke much about our time there other than talking about how good a club it was and how amazing the supporters where
12 Are you still coaching youths at Thistle/Rangers
Yeah I was asked to join Rangers and I moved in February after 30 amazing months at Patrick, I'm enjoying youth coaching at the moment but I want to work with 1st team players as that's always something I wanted to do after my career, I hope one day to be a manager so fingers crossed. Also coach 1st team at Clyde as well as still play
13 Any future plans?
Just to continue coaching and try and become a manager, maybe Dundee one day