No, the internal directory cannot be disabled, but you can prevent users from being added to it by changing your Jira mode to be private under general configuration. This will prevent users from signing up for an account and be added the internal directory automatically without you inviting them/creating their account.
Our Jira is already in Private. We wonder how they are getting invited
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Someone with Admin permissions can invite users via email, those users will be created in the internal directory, unless you have a external user directory that is setup with read/write permissions. User are also created in the internal directory if you import issues via csv for example. If Jira cannot resolve the username in your import, it will create a new user for you.
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If you look in the Audit log you should be able to tell who is adding users to your instance.
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In my scenario, the audit log shows "system" added user to Jira Internal Directory. Username was full email address.
10 days later I see where "system" added same user to Delegated LDAP Authentication. Username was just username without @company.com.
The problem becomes that now I have 2 jira users with same email address.
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