The 20-year old Italian, who won last week's BMW PGA Championship, added a 7-under 65 to his opening 66 for a 13-under total for two rounds on the Bro Hof Slott course in Stockholm.
Manassero capped his round with four birdies in succession from the 11th hole.
"It was nice after my good start to come back today and shoot another great score," he said. "I am glad the way the day has gone as I played solid. Over the last five or six holes I didn't feel as good as I did at the beginning but I was scoring well which is a good sign."
Finland's Mikko Ilonen is second at 11 under after birdieing his final three holes for a 9-under 63. He matched a new course record, set just hours earlier by Scotland's Peter Whiteford, who is third at 10 under.
It is the third time Ilonen has shot 63 in his career, while Whiteford's effort is the 32-year-old's lowest score in five full seasons competing on the European Tour and one shot lower than Lee Westwood's 64 en route to victory in the event last year.
"It was brilliant and a great round of golf, and it's put me in a good position though it's still a long way to go," Whiteford said. "The scoring looks like it will be low over the weekend but it's just great to be in contention again."
Whiteford came close to his first tour win a month ago, losing in a playoff for the Ballantine's Championship in South Korea.
He finished with a 65 to reach the 2-under mark and squeeze into the weekend rounds. Last year, Dodt secured the second-to-last order of merit position to retain full tour membership.
Among those missing the cut was Scotland's