A method of bonding composite structures includes positioning a second structure at a bonding site on a first structure and coupling a first vacuum bag to the first structure such that the first vacuum bag covers the bonding site. The method also includes applying a vacuum to the first vacuum bag to induce a first mechanical force to the second structure via the first vacuum bag. A second vacuum bag is coupled to the first structure such that second vacuum bag covers the second structure and at least a portion of the first vacuum bag. The method further includes applying a vacuum to the second vacuum bag to induce a second mechanical force to the second structure via the second vacuum bag.