Google not indexing main page because it's Duplicate, Google chose different canonical than user

Technical Q&A
,

Topic summary

Main issue: Google is de-indexing the site’s main page as a duplicate and selecting the default Shopify domain as the canonical URL instead of the custom domain (halo-lb.com).

Key details:

  • Google Search Console flags “Duplicate, Google chose different canonical than user.”
  • The canonical URL (the preferred version of a page for indexing) is being set by Google to the Shopify default domain, which the store owner says cannot be removed.
  • Screenshots show GSC status and Shopify domain settings.

Proposed causes (from replies):

  • Google initially indexed the old Shopify domain and kept it as canonical.
  • The theme may not include correct canonical HTML tags.
  • Another misconfiguration could be present.

Actions/owner response:

  • Owner set the main domain in Shopify, which should auto-manage canonicals.
  • GSC shows the user-declared canonical is the desired one, but Google still chooses the default domain.

Status and next steps:

  • No concrete fix identified in-thread; one responder suggests hiring a Shopify Partner to investigate.
  • Owner is considering removing the default Shopify link or other options. The issue remains unresolved.
Summarized with AI on January 3. AI used: gpt-5.
1

I have the following domain that is linked to my shopify store:

Recently the link has been removed from the Indexed page of Google console and is mentioned under:
Duplicate, Google chose different canonical than user.

The chosen canonical by Google is the default domain of shopify which can’t be removed.

How can I solve this?

joseph123123_0-1709473766358.png
joseph123123_0-1709473766358.png1627×1060 60.1 KB

joseph123123_1-1709473836651.png
joseph123123_1-1709473836651.png1294×475 31.7 KB

2

Hi @joseph123123

The problem could be caused by the following things:

  • Google originally indexed the website from the old Shopify domain for the canonical address.
  • Your theme has not physically put the necessary HTML to signal to Google a change in the canonical address.
  • Some sort of other misconfiguration.

Not sure on your level of expertise but if you don’t know how to fix it I highly recommend hiring a Shopify Partner like myself to help resolve the issue. Feel free to reach out to me on from my website or personally message me here on the forums.

3

Hello @sanico-software ,

Thank you for reaching out.

Shopify automatically manages the canonical configuration when setting the main domain. (Which I did the in screenshot)
Based on Google’s result, it’s mentioned that the User-decaled canonical is the one I want but Google still chooses to ignore it and set the default link.
I think I need to be able to completely remove the default link of my store or if there is any other suggestions.