The Welshman built on his opening round of 66 to reach the halfway way stage nine-under par after a 69 on Friday that included six birdies.
Donaldson has his sights set on a place in the European team for the Ryder Cup and this is the penultimate qualifying event for next month's showdown with the United States.
The 38-year-old occupies an automatic berth but is yet to be confirmed in Paul McGinley's line-up.
Starting at the 10th, Donaldson was one under at the turn before stringing together four birdies in six holes on the back nine to stretch his lead.
Two bogeys in the final three holes blotted his copybook, though, and Bourdy is well placed to deny Donaldson what would be his first win on tour this year.
"I played nicely again and made a lot of birdies out there today, but a few bogeys so if I can go out there tomorrow and play as well as I've played over the last couple of days I'll be in a strong position going into the final round," said Donaldson.
"Overall it was a solid day but like I said it could have been very good out there.
"I won't dwell on the poor shots; I played two pitches at seven and eight and misjudged them both so one's come out hot and one's come out dead. That slowed the run down, up until that point I was really motoring.
"It's a great golf course, it's generous off the tee and you're setting yourself up for birdies on a regular basis so it's more of the same and go and attack at the weekend."
Bourdy started his day with three successive birdies and, after picking up two more shots, he carded a five-under 67 to climb 11 places on the leaderboard.
A group of five players finished a further shot back, including Stephen Gallacher, one of Donaldson's rivals for a place at Gleneagles next month.
The Scot had a mixed start with two birdies being cancelled out by two bogeys, but he roared back into contention with five birdies on his back nine.
England's Tommy Fleetwood will also go into Saturday's round on seven under after he signed for a 65, the lowest round of the tournament, to move to within two strokes of the summit.
Mikael Lundberg, who was second after the first round, suffered terribly as he tumbled down the standings following a four-over 76.
Four bogeys and a double bogey blighted the Swede's round, but two birdies on the back nine ensured he just made the cut for the weekend.
It was a tough cut to make as a par score was the minimum requirement, and that proved out of the reach of the likes of Bernd Wiesberger, David Horsey and Simon Dyson, who were among the top-10-ranked players in the competition.