"I'm pleased that Leon is happy to sign for us and I'm looking forward to him meeting up with the rest of the squad again for pre-season," Flynn told the official Swansea website.
"His agent contacted me on Monday to let me know that he was accepting the offer we've made him, and he'll sign his contract next week when he arrives back from France.
"Leon only turned 20 just before he came to us on loan last season, but we saw him grow in confidence and stature with every appearance he made.
"I think he's going to enjoy being a member of the first-team squad and I'm confident that he'll make quite an impact."