Google Scholar Deindexing After Enabling RESTful URLs (OJS 3.5.0.1)

Software Support
1

We are currently using OJS 3.5.0.1 hosted in a subdirectory:

https://rootspress.org/journals

Recently, we enabled clean URLs by setting:

restful_urls = On

Previously, our journal URLs were structured as:

/journals/index.php/pbiotech/article/view/XXX

After enabling RESTful URLs, they changed to:

/journals/pbiotech/article/view/XXX

Proper 301 redirects from the old index.php URLs to the new clean URLs are working correctly via .htaccess.

Current Issue

After this change, we observed the following:

  1. Google Search still indexes many URLs under:

    site:rootspress.org/journals/index.php/pbiotech

    but shows no results under:

    site:rootspress.org/journals/pbiotech

  2. Google Scholar has removed most articles from indexing.

  3. There are no firewall, ModSecurity, CSF, or Imunify360 blocks (confirmed by hosting provider).

  4. Article pages return HTTP 200.

  5. Metadata tags (citation_*) are present and valid.

  6. OAI endpoints are working:

    /journals/index/oai
/journals/pbulletin/oai

  7. Robots.txt does not block crawling.

  8. No noindex directives are present.

  9. PDFs are publicly accessible and not behind login.

Our Questions

We would appreciate guidance on the following:

  1. Does enabling restful_urls = On in OJS 3.5 require any additional configuration to preserve Google Scholar indexing?

  2. Is there any recommended migration process when switching from index.php URLs to RESTful URLs to prevent Scholar deindexing?

  3. Does OJS automatically generate canonical tags for both URL versions, or should we manually ensure canonical consistency?

  4. Could enabling RESTful URLs trigger any internal route changes affecting sitemap generation or Scholar crawling?

  5. Is there an official PKP-recommended best practice for URL migration in production journals to avoid indexing loss?

Additional Technical Information

  • force_ssl = On

  • Clean 301 redirects confirmed

  • Shared hosting (Apache)

  • No changes to metadata templates

  • No change in article content or DOI structure

2

Changing URLs will temporarily remove publications from Google Scholar indexing. It will take some time to get back in. I think I read that Google indexes default URLs better than RESTful ones.

One way to speed up indexing is to use Google Search Console and add the sitemap.xml location there for your site. Google says:

Google will try to crawl a sitemap as soon as you submit it. If the request succeeds, Google will continue to recrawl the sitemap at a pace independent of the site crawl schedule.

While Google should find the publications, especially if you have the “Google Scholar Indexing Plugin", it can take some time.