The Englishman led the way on Thursday's opening day with a 68, giving him a one-shot advantage over a chasing pack of eight rivals.
The Oxfordshire 23-year-old played some of the best golf of his career at the challenging PGA Catalunya course.
He finished four-under to hint at adding to his one professional title to date - the 2012 Allianz Open Cotes d'Armor Bretagne.
But Pepperell, mostly to be seen playing in casual golf clothing , including tracksuit tops and sleeveless collared shirts, faced a tough challenge from those just behind him.
Bookies favourite Sergio Garcia led a cluster of players on three-under, including Spanish compatriots Rafael Cabrera-Bello and Miguel Angel Jimenez.
On day two, Pepperell, in only his second season, widened his lead during the opening 12 holes.
Beginning on the course's back nine, the first two holes were birdied and he followed this up by eagling the 12th, giving him a lead of five shots.
But then he double-bogeyed the 14th and 18th to leave him on 35 at round two's halfway point, one in front of Joost Luiten.
After 12 holes Pepperell enjoyed a three-stroke buffer from second-placed Briton James Morrison.
© Copyright Press Association
News brought to you by Glenmuir, add a touch of luxury to your golf game.
Experience the Glenmuir Men's Lined Water Repellent Golf Sweater