International SEO duplicate content issue for same content on different cctlds in the same language.

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Dear Shopify Community,

we are running a shopify store that currently holds 2 domains: 1 for Austria and 1 for Germany (.at and .de).

All of the content on every page including urls - except of the domain of course - is the same (because both in Austria and Germany people speak German)  . As far as we know shopify automatically ads hreflang tags to the website versions in order to make our blogposts show up in both countries for search queries.

However as soon as we added our new austrian domain to google search console, google recignized a canonical tag for all pages/blogs for the AUSTRIAN domain which resulted in our Blog/Pages using the German domain to get their indexing removed and reallocated to the Blog/Pages on the austrian domain.  This resulted in the destruction of all of our SEO efforts and organic traffick on the German market.

As far as we know HREFLANG tags are there to avoid this. They are there to show google that something isn't duplicate content but simply is targeted to another region. We contacted shopify and they told us that there is nothing wrong with our hreflang setup.

Still, we could find other people who share a similar problem. We think that shopify added a canonical tag to our austrian domain, which defeats the purpose of international SEO.

Is there anyone who could point us in the right direction or has already solved a similar issue?

Best regards