About deleting a custom security configuration
If you no longer need a custom security configuration, you can delete that configuration to ensure it will not be applied to any repositories in the future. If you are deleting a custom security configuration because you want to change the security enablement settings in that configuration, you can instead edit the configuration. For more information, see "Editing a custom security configuration."
Warning: Deleting a custom security configuration will detach all repositories that are linked to that configuration. The existing security settings for those repositories will be unchanged, but you must apply a different security configuration or manage their security settings at the repository level to keep their settings up to date.
Deleting a custom security configuration from your organization
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In the upper-right corner of GitHub, select your profile photo, then click Your organizations.
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Under your organization name, click Settings. If you cannot see the "Settings" tab, select the dropdown menu, then click Settings.
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In the "Security" section of the sidebar, select the Code security dropdown menu, then click Configurations.
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In the configurations table, click the name of the custom security configuration you want to delete.
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Scroll to the bottom of the "Security settings" section, then click Delete configuration.
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In the "Delete this configuration?" window, read the warning to confirm you are comfortable deleting the custom security configuration, then click Delete configuration.