The Northern Irishman arrived at Wentworth Club having won the previous two Rolex Series events but was in danger of heading home on Friday, sitting at level par after 35 holes.
In dramatic scenes on the 18th, he made the cut on the mark with a two-putt birdie as the scoreboard illuminated the putting surface in the quickly fading light.
The four-time Major winner went on to card a 67 on Saturday and even looked to have a chance of victory on Sunday, getting within two of the lead at one point in a closing 65.
And while he may not have got the second BMW PGA Championship he craved, McIlroy was pleased with his weekend's work ahead of teeing it up at Marco Simone Golf and Country Club in 12 days' time.
"It feels much better," he said. "It was nice to see the play better yesterday and again today, really happy with where my wedge play and iron play is.
"Over the weekend I started to hole some more putts, the weekend was great.
"I struggled a little bit Thursday and Friday but I've been saying it's not too far away. I was 16th in Ireland last week, not a fair reflection of how I actually played. I played well, just a couple of water balls on the back nine on Sunday.
"It's been two solid weeks and definitely things to improve and to work on. But everything's headed in the right direction.
"Certainly some good improvements over the weekend, and still some things to probably work on but definitely in a better spot with where everything is.
"I don't want to get too excited, there's still nearly two weeks to go before we tee it up on the Friday of The Ryder Cup. Still got plenty of time.
"I'll hang around here for the next week and get some really good work in Thursday, Friday, Saturday, Sunday before heading to Rome, which will be great.
"Once we get there, we still have four days of practice to do, so I'll certainly be chomping at the bit to get started."