The Scot fired five birdies in seven holes on the back nine to reach six under par and surpass the early clubhouse leader Ross Fisher, who made 66 in the morning wind and rain on a tough day of scoring in Farsø in northern Denmark.
MacIntyre got up and running with a birdie at the second and another courtesy of a superb approach to the fifth.
He alternated bogeys and birdies around the turn, dropping shots at the eighth and tenth but birdieing the ninth and 11th, the latter after a long bobbling putt from off the green, before holing from 32 feet at the 12th.
He hit the front with another pair of back-to-back birdies thanks to a good up-and-down from beside the 14th green and a long putt at the next.
Another from seven feet at the 17th took him two clear and he said: "I'm in a good mindset just now, I just pitched up here refreshed and with a good attitude.
“It was really tough today. When I was sat in my room this morning, I was quite glad that I wasn't out there. It got a little bit nicer. Obviously, the breeze was really strong, but at least we didn't have any rain.
"It was just a mental battle out there and just had to stay positive. The dropped shots were going to happen and just had to take the chances when they came and thankfully I did that. Bit of luck here and there.
"I've been working hard on the my game the last three weeks, I've chopped and changed. There's been a lot of changes and I've kind of gone back to what I know I'm good at. I've stayed positive and I knew my game was there, just had to drive the ball a little bit better this week.
“Probably on 12 was my best moment when I hit the putt slightly too firm and it was right in the middle of the hole the whole way but I was just praying it didn't bump offline."
Fisher was out in 33 with birdies at the second and sixth, otherwise parring every hole until the 13th before an eventful finish to his round.
The Englishman birdied the 14th and 15th, dropped a shot at the 97-yard 16th but regained it with an eight-foot putt at the next to finish four under.
“It's a good day,” he said. “We were just saying the weather was not very pleasant when we were waiting for the boys in front to tee off. Thankfully, we only had a couple of holes (in the rain), but the wind was really, really strong, it played tough.
“There wasn't much run on the fairways. Both the par fives were pretty much out of range. It was just nice to almost come through the round unscathed.
“Sixteen was a little disappointing, felt like I hit a really nice shot in there and but just left myself no putt off the top tier, but nice to bounce back with a birdie on 17. Disappointing not to hole that one on the last but if you'd have offered me four under when we pitched up this morning, I'll definitely take it.”
American Johannes Veerman produced a bogey-free round to share third place on three under with German Nick Bachem, a winner on this season’s DP World Tour at the Jonsson Workwear Open, and Dutchman Daan Huizing, a top-ten finisher at the recent BMW International Open.