By using a compliant QR code generator, of which there are many on the web.
This topic has come up a couple of times in recent months and that ID uses the 2.1 standard, which doesn't handle accented characters properly, was finally nailed down.
There was a workaround of editing the QR code fields, but really, the solution is to just use a better tool until ID's feature — which is really one of the courtesy, nice-to-have ones and not something integral to most workflows — is updated.
Which may happen. QR codes kind of did a 'dead cat bounce' from wildly popular to hardly used and now back to fairly selective, considered uses. I think Adobe added it in the first phase, consigned it to low priority in the second phase, and might update it to 3.0 now that it's stable and used just often enough.
— | Word & InDesign to Kindle & EPUB: a Pro Guide (Amazon)