Xdebug Error: "Failed loading xdebug.so: xdebug.so: cannot open shared object file: No such file or directory"

Even though you have the two sites split up and using two different php.ini files, CRON will still use whichever php.ini file the PHP-CLI is configured to use. So, to figure out which php.ini CRON is using, this is the command to use:

php -i | grep php.ini

If PHP-CLI happens to be using a php.ini file that you didn't expect it to be using (such as /usr/local/lib/php.ini) then that will be the key to figuring out why you're seeing Xdebug errors in the logs.

It turns out that the /usr/local/lib/php.ini file had these two values set:

extension_dir = "/usr/local/lib/php/extensions/no-debug-non-zts-20090626"
zend_extension = "xdebug.so"

That was causing the error from the php script that was run by CRON (i.e. PHP-CLI) because zend_extensions need the full path to the module. This is also stated in the Xdebug documentation: http://xdebug.org/docs/install

So, to get rid of the error, just comment out that line (or just remove it). You could also comment out or remove the extension_dir line as long as you are not loading any other modules such as:

extension = memcached.so 

Sometimes might be difficult from where the XDebug library is loaded since it can be done either by specifying the path in php.ini or by adding the lib in mods-available.

Firstly, run:

$ sudo grep 'xdebug' -r /etc/php/*

This will give you the files that loads the extension.

Now identify which php.ini is in use:

$ php -i | grep php.ini

This will give you the php version in use (in case you have multiple php versions). Now link the php version with the result from the first step.

Now, either you have to comment out the line where the xdebug extension is loaded or remove the xdebug.ini file (that loads the extension) from /etc/php/x.x/mods-available (where x.x stands for the php version in use).

For the record, in Linux Mint and I think in some Ubuntu Systems. To change the php.ini it's the best to go to /etc/php/7.0/cli/conf.d and look for the xdebug.ini and you must change the lines said in the post above mine.