Jim Colbert and Stewart Ginn finished one shot off the lead at 4-under-par 68. Jay Sigel and Darrell Kestner followed in a tie for fourth at 3-under-par 69.
Bean started on the back side at BosqueReal Country Club and tallied his first birdie of the day at the par-5 12th. At the par-4 15th, Bean dropped his approach inside seven feet and drained the birdie putt before adding a birdie at the 17th to make the turn at 3 under.
The 50-year-old continued his fine play on the front nine with back-to-back birdies starting at the par-4 third. He found trouble with a bogey at the fifth, however, but was able to respond with a birdie at the par-5 sixth.
Bean then hit a 9-iron within two feet of the cup for a birdie at the par-4 eighth to reach 6 under.
'The 9-iron on No. 8 was my best shot,' said Bean. 'It nearly went into the hole.'
He found trouble at the ninth, his last, and missed a four-foot par save for a closing bogey.
'All in all it was a very solid round,' said Bean, who amassed 11 victories in his time on the PGA Tour. 'I played a very good round. I look forward to the next two days.'
Colbert closed with a flurry of birdies for his share of second. He picked up a birdie at the 15th and ran home a 20-foot putt for a birdie at the very next hole.
The 62-year-old then hit his approach to 10 feet at the 17th and converted the birdie try to make it three in a row.
'I left a few putts short today,' said Colbert. 'I have to get through tomorrow before I can start thinking about Sunday and winning.'
Hale Irwin, the all-time leader in wins on the Champions Tour, collected four birdies and two bogeys for a round of 70. He was joined by Graham Marsh, Jack Spradlin, Jim Ahern and John Harris in a tie for sixth.
Reigning Senior PGA champion John Jacobs double-bogeyed the last to finish one shot further back at 1-under-par 71 along with Sam Torrance and Hugh Baiocchi.
Defending champion David Eger, who won for the first time on the Champions Tour at this event last year, came in at even-par 72 in a group that includes Champions Tour rookie Mark McNulty and Tom Kite.