Why Googlebot Ignores Some Canonical Tags: Hidden Conflicts Explained

The notification “Duplicate, Google chose a different canonical than the user” in GSC is one of the most frustrating notifications for an SEO professional or website owner. You may think that you did everything correctly by adding the rel=”canonical” tag with the declared version, and therefore, Google would recognise you as the authoritative source of the information. When Google did not do that, it indexed a URL that you did not want or excluded your content entirely.

The reason this occurs is due to how Google’s indexing algorithms work. To understand why Google made this decision, an in-depth examination of the hierarchy of signals used by Google to determine which version of a particular web page is the primary page is required.

This guide explains the underlying issues that cause this type of error, describes the function of the canonical tag in the protocol used by Google to index web pages, and offers guidance on troubleshooting indexing issues resulting from Google’s determination of a primary version.

The Core Concept: A Hint, Not a Directive

To see why Google does not give weight to canonical tags in its ranking system, you must first accept the basic concept of search engine optimisation (SEO): that a canonical tag is an indicator, or signal, and not a declarative or directive statement.

When RFC 6596 was created as a standard format for using a canonical tag to identify duplicate content on a site, it was intended to offer assistance to the search engines in sorting through the duplication of content and determining which page(s) to include in the final search results. 

But for Google, the canonical tag is only one of many indicators that it uses when assessing a page’s ranking. The primary goal of Google and the search engines is to find and present the content that will provide the user with the greatest value and best overall user experience. 

Therefore, if the algorithms of Google find that another site offers the best user experience or if the signals sent by different sites do not match, they will replace the manual choice made by the web master and choose the best option instead.

Google evaluates a “cluster” of duplicate pages and calculates a score for each URL based on several weight-bearing factors:

• The rel=”canonical” tag itself.
• Internal linking patterns.
• Sitemap inclusion.
• Redirects.
• HTTP vs. HTTPS preference.
• URL shortness and clarity.

If these signals do not align perfectly, Googlebot’s confidence in your canonical tag drops, leading it to make its own decision.

Conflict 1: The Sitemap Paradox

One of the most common reasons Google overrides your preference is a conflict between your HTML tags and your XML sitemap.

Your sitemap is effectively a list of the pages you consider most important. When you include a URL in your sitemap, you are telling Google, “This page is vital; please index it.”

The Contradiction

A significant issue will develop with the difference between a canonical link and a sitemap URL. An example of this situation is having one page (Page A) that has a canonical link pointing to another page (Page B), but the only page included in your sitemap is Page A.

As a result, you are sending an ambiguous message. The canonical link is telling Google to “Index Page B” whilst at the same time, the sitemap indicates to Google to “Index Page A”.

As you can see, this is contradictory. In these cases, Google usually will disregard your canonical instructions. Generally, Google will trust the information contained in the sitemap, as this is a “discovery” signal, and treat the on-page canonical link as potentially erroneous.

Best Practice

Ensure that only self-canonicalising URLs (pages that point to themselves) are included in your sitemap. If a page canonicalises to a different URL, it should generally be excluded from the XML sitemap to prevent signal confusion.

Conflict 2: Internal Linking Structure

The way your website’s pages interconnect creates a vote for how authoritative each page of your website is. Basically, when someone clicks on an internal link, it sends page rank from the source (the old page) to the destination (the new page).

For example, if you set your canonical tag placement for your “Variant URL” to point to your “Main URL” but did not set up an internal linking structure where all the links on your navigation bar, footer, and blogs pointed to the “Variant URL,” you would not be properly following the instructions for canonical tagging.

Google is looking at a user journey; therefore, if users are continually led to the “Variant” page through your internal menu structure, Google is interpreting this as an indication that the “Variant” page is the primary or preferred page.

Why does Google consistently ignore canonical tagging in this situation? Because your technical foundation suggests to Google that your canonical tag placement is incorrect. This means to resolve this issue, you must set up your entire internal linking structure to consistently point to the URL destination you want indexed.

Conflict 3: The Problem of Multiple Canonical Tags

The problem of technical implementation errors is often caused by the presence of multiple canonical tags included within the markup source code of a web page.

In general, multiple canonical tags on a single page will occur when there is a problem with the relationship between a website’s CMS, its theme and the website’s SEO plugins; for example:

• A WordPress theme can hard-code a canonical.
• The CMS plugin(s) will typically insert a canonical into a web page that has been created using a specific SEO plug-in (e.g., Yoast or RankMath).
• A programmer or developer may have added a canonical tag to the webpage by manually inserting it into the document via a header injection script.

Whenever Googlebot encounters a webpage containing several canonical tags, it is unable to determine which of those canonical tags you intended to establish as your “official” canonical and because of that, most of the time, Googlebot will ignore all of them. While in some error situations, Google may attempt to interpret or guess which tag is likely the correct one to select for indexing and ranking, when multiple canonical tags are detected, Google does not utilise any of those tags for any other reason than to ignore all of them.

As a result, the algorithm does not have an appropriate set of criteria to determine which version of each URL should be indexed, so it ultimately uses some combination of other signals (such as content quality, and inbound link counts) to determine the appropriate URLs for indexing, thus eliminating your ability to make a choice regarding which canonical tag should be selected for indexing.

Conflict 4: Incorrect Canonical Tag Placement

The location of the code matters just as much as the code itself. According to HTML standards and Google’s guidelines, the rel=”canonical” tag must appear within the <head> section of the document.

Common placement errors:

• In the Body: If the tag is placed inside the <body> section, Google will simply ignore it. This often happens when users try to insert SEO tags using widgets or content blocks rather than theme headers.
• Too Low in the Head: If the <head> section is cluttered with massive scripts or CSS, and the canonical tag is pushed too far down, there is a risk that the rendering process might time out or cut off before reading the tag.

To make sure your proper canonical tag placement is the best it can be, put them at the beginning of your HTML document so they will be read first as they are being parsed. If you are inserting canonical tags through client-side rendering via JavaScript, you increase the chance that the canonical will be missed or delayed. This could result in Google interpreting the page as originally having no declared canonical.

Conflict 5: Content Parity and Quality

To address issues stemming from duplicate content that is in fact canonised, Google has provided a means for webmasters to resolve their duplication problem through canonicalization. 

For example, if you point a canonical tag on Page A to Page B and the content of Page B is not like that of Page A, then Google won’t see Page B as being the same page or even closely related, and therefore will not consider this tag as a legitimate method to consolidate the authority of Page A into Page B. 

Canonical tags were developed to help webmasters avoid the canonical duplicate content issues that arise when multiple web pages are publishing similar or identical content (e.g., mobile vs. desktop or print versions of the same content) or have related sorting parameters in their URLs.

If you try to consolidate the authority of an old article with the new article by using the canonical tag, Google will treat this as a “soft 404” or otherwise categorise the canonical tag that was used as a bad canonical. Does Google ignore such tags as a form of ranking manipulation for unrelated article contents? Yes, nearly always.

The E-Commerce Challenge: Permutations and Parameters

It is challenging to implement Canonical Strategies effectively in the e-commerce SEO mix. E-commerce retailers often create thousands of URL variations from filter combinations (colour, size, price, etc.) and search options.  In the examples below, you can see the difference between the Main URL and the Variant URLs:  

• Main URL: example.com/shoes  
• Variant: example.com/shoes?color=red  
• Variant: example.com/shoes?sort=price_asc  

When the main canonical tag fails to self-canonicalise on the root category page or the platform has multiple dynamically generated canonical tags created for all filter combinations, Google may decide to index a filtered version (for example, the Red Shoes page) instead of indexing the main category page. The reason for this decision is usually due to the influence of external backlinks to the specific URL of a filtered view. 

If an external source, such as a highly-trafficked blog, sends a link to your URL with the parameter of ?sort=price_asc, Google will see that as a strong indication that this specific filtered view is a more relevant result. If you do not create strong internal canonical tags to direct Google to your main product pages, it will give more weight to external backlinks to filtered views.

HTTPS and URL Structure Preferences

All else being equal, Google has a hard-coded preference for:

1. HTTPS over HTTP: If you canonicalise an HTTPS page to an HTTP version (or vice versa, but serve both), Google will almost always choose the HTTPS version.
2. Short URLs over Long URLs: Google prefers cleaner, shorter URLs. If you canonicalise a clean URL to a long, parameter-heavy URL, Google might ignore it in favour of the cleaner version.

This “tie-breaker” logic is often why Google ignore canonical requests even when other signals seem fine.

Troubleshooting: How to Inspect and Fix

If you suspect Google is ignoring your tags, you need to move from theory to investigation.

Step 1: The URL Inspection Tool

Open Google Search Console and inspect the URL you want to be canonical. Then inspect the URL that Google actually selected. Look at the “Page Indexing” section. It will show two lines:

• User-declared canonical: What you asked for.
• Google-selected canonical: What Google chose.

Step 2: Check for Sitemap Conflicts

Verify if your canonical in sitemap strategy is consistent. Ensure the URL Google chose is the one in the sitemap. If not, update your sitemap to reflect your preferred URL.

Step 3: Audit for Multiple Tags

View the source code (Ctrl+U) of the affected page and search for “canonical”. If you see the string appear more than once with different URLs, you have multiple canonical tags. You must audit your plugins and theme files to remove the duplicate injection.

Step 4: Review Internal Links

Run a crawl of your site (using tools like Screaming Frog). Check the “Inlinks” for the page Google is ignoring. Are you linking to the wrong version? Update your internal anchors to point to the correct canonical tag placement.

Conclusion: Aligning the Signals

The question “Does Google ignore canonical tags?” is essentially a question of signal consistency. Googlebot is a sophisticated detective; it gathers evidence from your sitemap, your links, your code, and your content. When the evidence contradicts your testimony (the canonical tag), the detective ignores you.

To master canonical tag selection, you must ensure that every signal points in the same direction.

1. Place the tag high in the <head>.
2. Avoid multiple canonical tags.
3. Ensure the canonical in the sitemap matches the page tag.
4. Align internal linking to support the canonical version.
5. Use e-commerce SEO canonical best practices to manage facets and filters.

By harmonising these elements, you force Google to respect your site architecture. Whether you are managing a local blog or a massive enterprise site handling SEO services in Dubai, maintaining clean canonical signals is the bedrock of index stability and crawl budget optimisation.