Defending champion Ian Poulter played with Montgomerie and posted a 3-under 68. He stands alongside Sergio Garcia at 7-under-par 135.
Montgomerie is trying to win his eighth Order of Merit title this week at Valderrama Golf Club. He is battling U.S. Open champion Michael Campbell for the Order of Merit crown and leads Campbell by eight shots entering the weekend.
'Michael is a world (class) player and is capable of scoring two good scores over the weekend,' said Montgomerie. 'I've got to counteract that and that is my job this weekend. I've just got to keep doing the same thing. It is a stress, a huge stress and I'll be glad when Sunday evening arrives whether I win this thing or not.'
The Scotsman shared the lead entering the round with Poulter. Before they teed off, Garcia had birdied the third to join them at 4 under.
Montgomerie, however, quickly took the lead by himself. He knocked his approach to the first within 2 feet to set up birdie. After Poulter birdied the second, Montgomerie sank a 7-foot birdie putt on the third to get to 6 under.
The 42-year-old moved two strokes clear of the field with a 10-foot birdie putt on the fourth. Montgomerie, who holed out for eagle on the par-4 eighth on Thursday, dropped his second shot 2 feet from the cup on the same hole for his fourth birdie of the day.
'Well to almost hole your second shot on the first, I'd say that was almost a perfect start,' Montgomerie said. 'I birdied one, three, four and eight and was 4 under after eight, so yeah, that was a good round of golf.'
Around the turn, there were two big swings on the 10th and 11th. Poulter played the front nine in 2 under to turn at 6 under. His approach to the 10th stopped 25 feet from the cup.
Poulter ran home that putt for birdie to get to 7 under. Meanwhile, Montgomerie's second shot spun off the green and back down the fairway. He chipped to the front edge of the green, then two-putted for bogey to fall into a share of the lead at minus-7 with Poulter.
Montgomerie sank a 6-foot birdie putt on the next to reclaim the lead. It became a two-stroke swing as Poulter three-putted for bogey from the front edge to drop back to 6 under. Montgomerie ran home an 18-foot birdie putt on the 13th to grab a three-stroke lead.
He made it two in a row as his 17-foot birdie effort found the bottom of the cup at the next. Montgomerie parred his next three holes before a three-putt bogey at the last dropped his lead to two strokes.
'This is a very, very difficult course,' said Montgomerie. 'Our most difficult course in Europe to score on and I'm delighted to be 9 under par. Experience counts here.'
Poulter meanwhile, birdied the 14th for the second round in a row to get back to 7 under. He parred out from there.
After his birdie on the third, Garcia didn't post another birdie until the 10th. He then birdied 11 to move to 6 under. The Spaniard birdied 16 and 17 to put pressure on Montgomerie, but he bogeyed the last to end two back.
Lee Westwood and Paul Broadhurst each carded rounds of 2-under 69 to move into a tie for seventh at 2-under-par 140. They were joined there by Niclas Fasth and Jose Maria Olazabal.
Campbell shot 69 to get into red figures at minus-1. He was joined there by Luke Donald and Nick Dougherty.