Hybrid bonding systems and methods for semiconductor wafers are disclosed. In one embodiment, a hybrid bonding system for semiconductor wafers includes a chamber and a plurality of sub-chambers disposed within the chamber. A robotics handler is disposed within the chamber that is adapted to move a plurality of semiconductor wafers within the chamber between the plurality of sub-chambers. The plurality of sub-chambers includes a first sub-chamber adapted to remove a protection layer from the plurality of semiconductor wafers, and a second sub-chamber adapted to activate top surfaces of the plurality of semiconductor wafers prior to hybrid bonding the plurality of semiconductor wafers together. The plurality of sub-chambers also includes a third sub-chamber adapted to align the plurality of semiconductor wafers and hybrid bond the plurality of semiconductor wafers together.