Google uses UTF-8 it as default for their very popular encoder. From what I can see they don't even add the byte order mark.

The problem is that most scanners still seem to use JIS8 (QR 2000) instead of iso-8859 (QR 2005) as default, so it mostly does not work to use iso-8859 for encoding.

It seems like utf-8 is the only choice even if it is against the specification.

edit: I will go with utf-8 without ECI and without BOM. Against all spec and spirit but works best at the moment.

encoding utf-8 character-encoding qr-code iso-8859-1
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