In your Service desk configuration, in the people section, you should be able to configure the groups and people that have access to your service desk portal in the ''Service Desk Customers'' role.
After that you just have to make sure that they don,t otherwise have access to the issues in your permission scheme (remove them from the browse projects permission) and that should do the trick.
Its, if you're referring to the "internal" JIRA application view and Global Header menu options, only users defined as Agents will be allowed to actually view the JSD interface menu options (Queues, read-only SLAs, read-only Reports, and the ability to work on tickets in JSD projects). Managing Agents
Your non-Agent users may only raise a request via the JIRA Service Desk drop-down in the Global Header.
FYI - Users must be in the project Administrators role to configure items such as the Portal, SLAs, etc. JSD for admins
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