‘Disintegration’—the reversal of transposon DNA integration at a target site—is regarded as an abortive off-pathway reaction. Here we challenge this view with a biochemical investigation of the mechanism of protospacer insertion by the Streptococcus pyogenes Cas1-Cas2 complex, which is mechanistically analogous to DNA transposition. In supercoiled target sites, the predominant outcome is the disintegration of one-ended insertions that fail to complete the second integration event. In linear target sites, one-ended insertions far outnumber complete proto-spacer insertions. The second insertion event is most often accompanied by disintegration of the first, mediated either by the 3’-hydroxyl exposed during integration or by water. One-ended integration intermediates may mature into complete spacer insertions via DNA repair pathways that are also involved in transposon mobility. We propose that disintegration-promoted integration is functionally important in the adaptive phase of CRISPR-mediated bacterial immunity, and perhaps in other analogous transposition reactions.