Change PHP_INI_SYSTEM configuration settings
PHP_INI_SYSTEM level settings cannot be changed from .user.ini or ini_set function. To make change for PHP_INI_SYSTEM settings on Azure web app, follow the steps,
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Add an App Setting to your Web App with the key PHP_INI_SCAN_DIR and value d:\home\site\ini
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Create an settings.ini file using Kudu Console (http://<site-name>.scm.azurewebsite.net) in the d:\home\site\ini directory.
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Add configuration settings to the settings.ini file using the same syntax you would use in a php.ini file. For example, if you wanted to point the curl.cainfo setting to a *.crt file and set ‘wincache.maxfilesize’ setting to 512K, your settings.ini file would contain this text:
; Example Settings curl.cainfo=”%ProgramFiles(x86)%\Git\bin\curl-ca-bundle.crt” wincache.maxfilesize=512
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Restart your Web App to load the changes
Reference: https://docs.microsoft.com/en-us/azure/app-service/web-sites-php-configure