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

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Topic summary

Issue: Two Shopify ccTLDs (.de and .at) serve identical German content. After adding the Austrian domain to Google Search Console, Google selected the Austrian pages as canonical for all equivalents, causing the German pages to be deindexed and German organic traffic to drop.

Context: Shopify auto-adds hreflang (signals language/region alternatives) and appears to set canonical tags (signals the single preferred URL). Merchant expected hreflang to prevent duplicate-content issues across regions. Shopify support says the hreflang setup is correct. Merchant suspects cross-domain canonicals favoring .at.

Advice shared:

  • Audit each page’s hreflang alternates and canonical targets to ensure they don’t conflict.
  • Manually review critical URLs to catch misconfigurations.
  • Consider using tooling (e.g., an SEO app) for on-page checks and consistency, though it’s not a direct fix.

Status: No confirmed resolution. Key open question: how to configure canonicals and hreflang so Google treats .de and .at as regional equivalents without consolidating to the Austrian domain.

Notes: No images/code central to understanding.

Summarized with AI on January 1. AI used: gpt-5.
1

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

2

Hi @entspannend ,

Facing duplicate content issues across different domains targeted at specific regions like Austria and Germany can indeed undermine SEO efforts, despite correct hreflang tag setups. It seems like the canonical tags are pointing to one domain over the other, potentially confusing search engines about which version to prioritize.

To address this, ensuring both your hreflang and canonical tags are correctly set up is crucial. For each page, specify alternate versions with hreflang tags and use canonical tags wisely to avoid self-referencing issues. Sometimes, manually reviewing these tags for critical pages can help identify and correct misconfigurations.

In this context, SEOPro could be beneficial by providing insights into on-page SEO elements that may affect how search engines understand your site structure and content. While SEOPro primarily focuses on optimizing Shopify products and collections, its tools for bulk editing and SEO scoring can indirectly support the maintenance of a healthy site structure by ensuring consistency in how your content is presented to search engines.

Full disclosure: We are the developer of this app.