In SJU on the way home, you get your bags, take them to be scanned (a quick step - I believe it is an FDA scanner), recheck them with your airline, head to US customs and immigration, and then to your gate. I may be missing security - I can't recall if we had to go through security again - someone help me here. We have only flown through SJU once, but overall we preferred this route and will be doing it again this June with a 1.5 hour layover - fingers crossed. Hope this helps. Steve