Afobe, 19, has put pen to paper on his contract at the Reebok Stadium after returning from Arsenal's tour of Asia, where he played in friendlies against Malaysia XI, Manchester City and Kitchee FC.
Bolton manager Owen Coyle said: "Benik is a very exciting addition to our squad for this season and once again we would like to thank Arsenal and Arsene Wenger for agreeing to the loan.
"He's only 19 years old and you can see already that he is going to be a very good player. He has an eye for goal, is an athletic striker and there is much more to come from him."
Afobe, who has been on Arsenal's books since 2001, has had loan spells at Huddersfield and Reading in the last two seasons.
He scored eight goals in 35 games for Huddersfield in the 2010/11 season and played three times for Reading during the final weeks of their promotion-winning campaign.