Starting with JIRA 7, Atlassian introduced the new concept of applications. This turns Jira into a platform, and major features, such as JIRA Agile (now called Jira Software) and Jira Service Desk, are now separate applications that run on the Jira platform. These changes mean that you can now control user access to each of the applications individually. Instead of using permissions to control who can access Jira, you can assign access rights based on the application.
When it comes to granting access to applications, you can only do that through groups. So, you need to ensure that you have designed your groups appropriately in order for users to have access to the correct applications.
If you are in a group with Jira Administrators global permission (refer to the next recipe), such as jira-administrators, but the group does not have access to the Jira Software application, then you will still be able to log in to Jira and perform administrative tasks, but you will not have access to any projects and issues.