England’s Harry Hall occupies second place thanks to a 64, with compatriots Matt Fitzpatrick and Marco Penge one further back alongside Swede Ludvig Aberg.
US Open winner JJ Spaun missed the cut after a 72 left the American two over and Collin Morikawa tumbled out on four over following a horror 76.
Rory McIlroy, who benefitted from the benign early conditions, made a charge with a 65 to reach seven under.
“The conditions were so good for us this morning,” said McIlroy. “It felt like if you didn’t play that first nine in three or four under, you were losing strokes to the field.
“I did a lot of good things today, a couple of loose shots here and there but overall it was a good day. I’m excited for the weekend, right in contention.”
The afternoon starters had it tougher as the wind picked up at the sun-baked East Lothian venue and Scottie Scheffler, who was playing alongside MacIntyre, mixed five birdies with three bogeys in a 68 to sit five under at the halfway stage.
Gotterup, the world number 158, recorded nine birdies in a bogey-free second round to set the early target that makes him the man to catch.
Gotterup was threatening to break 60 after his ninth birdie of the day on 14, but four pars followed.
“It [59] never really crossed my mind,” said the 25-year-old.
“I made the putt on 14 and I was like, all right, I’ve got 16 and obviously 17 and 18 are pretty tough. So I really wanted to get 16.
“I’m not going to complain too much when I make my birdies on a course that isn’t always typically easy.”
