The main addition is the second set of boxes separate from the first set Qbby puts out. If Qbby tries to put out a third, the original disappears. The first set is green while the second set is blue-green. The two sets of boxes enable new puzzles as well as new spins on old mechanics. For instance, Qbby may need to press a button to open a gate but use a separate set of blocks to get up a platform.
The player can dress up Qbby in a different costumes purchased from the ingame store that uses currency from beating the levels
Players of the original can import costumes from the original if they have save data with them.
BoxBoxBoy! received "generally favorable" reviews on Metacritic getting a metascore of 80/100 based on 26 critics. On whatoplay.com, it receives an aggregate score (playscore) of 8.22 based on 20 critics.