Added a canonical ref tag and SERPs tanked, should we change it back?

[TienB24]

My client's CMS uses an internal linking structure that includes index.php at the end of the URLs. The site also works using SEO-friendly URLs without index.php, so the SEO tool identified a duplicate content issue.

Their marketing team thought the pages with index.php would have better link equity and rank higher, so they added a canonical ref tag, making the index.php version of the pages the canonical page. As a result, the site dropped in the rankings by a LOT and has not recovered in the last 3-months.

It appears that Google had automatically selected the SEO-friendly URLs as the canonical page, and by switching, it re-indexed the entire site.

The question we have is, should they change it back? Or will this cause the site to be reindexed again, resulting in an even lower ranking?

[dazonntechnolog]

Yes, I think you should change it back. Because canonical tags affect SEO from two points of view. For once, they directly influence how search results are displayed. The SEO tool found a duplicate content problem because the website also functions with SEO-friendly URLs that do not include index.php. Canonical tags have multiple benefits only when they are implemented correctly. So, please check your ref tag again and change it accordingly.

[Muffaddal]

What is the technical limitation? consider 301 redirects from index.php to seo-friendly urls