Jira Cloud Users & Groups Provisioning: Azure AD / Entra ID Sync Guide (REST API)

The miniOrange SCIM Provisioning, User Sync & Group Sync app connects Jira to Azure Active Directory (Entra ID) so user and group information flows into your Jira instance automatically. This guide covers the REST API integration method, in which the app pulls users and groups directly from Azure AD using a registered application's credentials. Once configured, accounts managed in Azure AD are reflected in Jira, so admins maintain identities in one place. Sync can run manually or on a schedule.

Before you begin

  • You need admin access to both your Jira Cloud site and your Microsoft Entra ID portal.

Download and Installation

  • Log into your Jira instance as admin.
  • Under Apps section, Click on Explore more apps.
  • Search for miniOrange SCIM.
  • Click Try it free to begin a new trial of the app.
  • After installation, locate the miniOrange Users & Groups Provisioning For Jira app and click to open it.

1: Admin Setup Configuration

Admin Setup Button

Upon installing the miniOrange Users & Groups Provisioning For Jira app, the admin needs to configure the Admin Token and API Key to complete the admin setup and start the provisioning process.


Note: The Atlassian API key is needed when provisioning or managing verified domain users or managed users. 

Part A: Configure Atlassian API Token

  • Go to Atlassian Account and login with your admin account.
  • Create API Token without scope and save at a safe place.
  • Create API Token in Atlassian
  • Go to Admin Setup page inside plugin and edit API Token Configuration (using pencil button)
  • Admin Setup Page
  • Enter your Atlassian admin Email Address, API Token, and expiry date of API Token.
  • Configure API Token
  • Click on Save Token.

Part B: Configure Atlassian API Key

  • Go to Atlassian Administration
  • Select your organization if you have more than one.
  • Navigate to Organization settings → API Keys
  • Click "Create API Key" and select "API keys without scopes"
  • Name API Key
  • Go to Admin Setup page inside plugin and edit API Key Configuration (using pencil button)
  • Enter API Key and click on Save API Key button. 
  • Configure API Key

Once these configurations are fully processed, your core administrative setup is complete and ready for application configuration.

2: Set up Microsoft Entra ID

Now you can proceed to establish a connection with Microsoft Entra ID.

Sign in to the Azure portal (https://portal.azure.com) as an admin, then open Microsoft Entra ID (Azure Active Directory).

In the sidebar, go to App registrations and click New registration.


Entra ID App Registrations
  • Enter a Name (e.g., Jira User Sync).
  • Under Supported account types, select the option that matches your organization (typically single tenant).
  • Click Register.
  • Entra ID Register an Application

    On the app's Overview page, copy the Application (client) ID and the Directory (tenant) ID. You'll need both in Step 4.

    Entra ID Application Overview

    Create a client secret:

  • Go to Certificates & secrets → Client secrets and click New client secret.
  • Entra ID Client Secrets
  • Add a description and expiry, then click Add.
  • Entra ID Add Client Secret
  • Copy the secret Value immediately. Azure will not show it again.
  • Client Secret List

    Grant the app permission to read users and groups:

  • Go to API permissions → Add a permission → Microsoft Graph → Application permissions.
  • Add the permissions the app needs to read directory data, for example: User.Read.All, Group.Read.All, and Directory.Read.All.
  • Entra ID API Permissions
  • Click Grant admin consent for your tenant so the permissions take effect.

Keep the Client ID, Client Secret, and Tenant ID handy for the next step.

3: Service Provider Configuration (Jira)

Now switch back to your Jira tab.


bullet 3.1 Application Configuration

  • Navigate back to the Configured Application tab on the main dashboard and click the + Add New App button.
  • From the Configure Application directory screen, locate and select Azure Active Directory as your chosen provider.
  • Select Entra ID from provider directory
  • Choose your integration method. Select REST API (custom integration workflow) then click Continue.
  • Select Integration for Entra ID
  • In the App Configuration wizard > Application Configuration section enter,
  • Field Value
    Application Name A unique label for this REST API application
    Client ID The Application (client) ID from Step 3
    Client Secret The client secret Value from Step 3
    Tenant ID The Directory (tenant) ID from Step 3
    REST API App Config for Entra ID

bullet 3.2 Provisioning Operations

In the Provisioning Operations section, define your synchronization settings:

  • Azure AD Directory: sync all users in the tenant.
  • Azure AD Enterprise Application: sync only users assigned to a specific enterprise application.
  • Azure AD Groups: sync only users belonging to specific groups.
  • Synchronization Config for Entra ID

Azure AD Enterprise Application (optional)

  • Enter the Enterprise Application Object ID from Azure AD to synchronize users and groups assigned to that enterprise application.
  • Users and groups assigned to the specified enterprise application will be provisioned to the application.
  • Sync Users from Application for Entra ID

Azure AD Groups (optional)

  • Enter the names of the Azure groups from which you want to sync users.
  • Press Enter after entering each group name to add multiple groups. Group names are case-sensitive.
  • Sync Users from Groups for Entra ID

    Once this is selected, click on Next.

User Operations:

Ensure the Import Users toggle is switched ON. In the Deactivated User Action dropdown, select the action that should be taken when a user is unassigned or deactivated in Azure.

User Provisioning Options

Group Operations:

  • Switch to Group Operations and enable Import Groups.
  • Group operations can be performed either with On-the-Fly Group Mapping or Manual Group Mapping.

1. On the Fly Group Mapping:

  • Select this tab to create groups dynamically as it is from IdP to Jira Cloud if they do not exist in Jira and map the users accordingly.
  • You can enable the Apply Regular Expressions on Group Names option to transform group names using Regex patterns before mapping them to Jira groups.
  • Under Filter Incoming Groups, you can configure how you want to filter group names received from the provider.
  • Group Provisioning Operations

2. Manual Group Mapping:

To map groups from your IdP to Jira's native groups, select this tab. When the sync executes, the users from respective groups of the IdP will be mapped to Jira groups as per configuration.

Manual Group Mapping
Note: Any unmapped groups left blank within this mapping list will be safely ignored when saving your profile.

Keep Existing Groups

This setting controls how a user's Jira group memberships are managed during user provisioning and deprovisioning operations performed by the Identity Provider (IdP).

Keep Existing Groups

Enabled:

For any new user added to IdP groups, it will be added to Jira groups. But if users are removed from IdP groups, Jira group memberships are preserved in the Jira directory.

  • Current Jira groups: jira-software-users, jira-administrators
  • Groups received from Azure AD: developers, employees
  • Resulting Jira groups: jira-software-users, jira-administrators, developers, employees

Disabled:

During provisioning, deprovisioning, or user unassignment, all existing Jira group memberships are removed except those specified in the Exclude Groups list. During provisioning, the user is subsequently assigned only to the groups received from the Identity Provider (IdP).

  • Current Jira groups: jira-software-users, jira-administrators, support-team
  • Groups received from Azure AD: developers, employees
  • Excluded groups: jira-administrators
  • Resulting Jira groups after provisioning: jira-administrators, developers, employees

After provisioning, the groups jira-software-users and support-team are removed because they are not received from the IdP and are not included in the exclusion list.


Exclude Groups: Use the Exclude Groups option to specify Jira groups that should never be removed during provisioning or deprovisioning operations, such as jira-administrators or org-admins. These groups will always be retained regardless of the user's group assignments in the IdP.


Scheduler Option:

To enable dynamic data synchronization at scheduled intervals, set Automate Synchronization to ON and define the processing interval by entering the desired number of days in the Synchronization Cycle (Days) field.

Scheduler

bullet 3.3 Review and Save Configuration

  • On the Review & Submit summary page, review your mapping details across the Application Configuration and Provisioning Operations summary tables to make sure everything looks right.
  • Click the Save Configuration button in the bottom right corner.

bullet 3.4 Run the Synchronization

  • Return to the Configured App Tab.
  • Click Synchronize on your Azure app.
  • When the sync completes,verify the new and updated users under Jira’s user management section.
  • If you set a scheduler in step 7,no manual action is needed for future syncs.

bullet 3.5 Verification

  • The app profile will appear on your main dashboard.
  • Under the actions column for your new entry, run a sync (or wait for the scheduled cycle if the Scheduler is enabled).
  • In Jira, navigate to User Management and confirm that users and groups from Azure appear in the directory. You can also review sync activity under the Audit Logs tab of the Plugin app.

The miniOrange Users & Groups Provisioning For Jira app is now successfully set up with Azure via REST API.

Did this page help you?

miniOrange Atlassian Contact Us

Book a Free Consultation with
Our Experts Today!

Schedule a call now!


Contact Us