Baisoya, a six-time winner on the PGTI, was one clear of the rest of the field at 12-under-128.
It was a crowded leaderboard as there was a four-way tie for the second spot at 11-under-129 between Delhi's Rashid Khan (64), Bangladesh's Badal Hossain (66), Chandigarh's Karandeep Kochhar (66) and Faridabad-based Karan Pratap Singh (67).
The day's best round of 63 was posted by Delhi's Himmat Rai, Bengaluru's Trishul Chinnappa and Sri Lankan N Thangaraja. While Himmat occupied tied sixth place at 10-under-130, Trishul was tied ninth at nine-under-131 and Thangaraja was tied 20th at six-under-134.
The cut went at two-under-138 and 51 professionals made the cut.
Honey Baisoya (64-64) jumped five spots from his overnight tied sixth thanks to his dogged 64. Honey, who won his last event about a year back, dropped an early bogey on the first where his drive found the trees.
The 22-year-old Baisoya was one-over through four holes before he charted a splendid recovery with consecutive birdies on the fifth, sixth and seventh. Honey missed an ace on the sixth as his magnificent tee shot stopped inches from the hole.
After another dropped shot on the eighth, Baisoya hit top-gear on the inward nine with five birdies courtesy some accurate drives and approach shots.
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