The Tool Desk
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Know what each control does
- SAML SSO sends sign-in for covered Atlassian accounts through your identity provider (IdP). Configure SSO and then enforce it through an Atlassian authentication policy. SSO alone does not deactivate accounts when someone leaves your organization.
- SCIM provisioning synchronizes supported account lifecycle changes, including account creation, updates, and deactivation. It does not provide SSO by itself. Atlassian documents group synchronization for Jira app instances and Confluence, but not Bitbucket or Trello. Atlassian’s SAML setup guidance and SCIM provisioning instructions describe these separate functions.
- Conditional Access evaluates sign-in context in the IdP and can require controls such as MFA or a compliant device, or block access. It is not an Atlassian-native setting. Microsoft Entra is one example; other providers have their own policy systems.
Account provisioning and application authorization are also distinct: a synchronized user or group does not automatically receive access to every Atlassian app. Map the appropriate users or groups to Atlassian app access.
Check prerequisites and plan the rollout
Atlassian’s documented SAML and SCIM setup flows list Atlassian Guard Standard, an organization administrator, an IdP directory, and verified and linked domains among the prerequisites. SCIM setup also requires administration of at least one Jira or Confluence site so you can grant synced users app access. Confirm the current plan and tenant requirements in Atlassian Administration before changing settings; plan capabilities can change. See Atlassian Guard details and its identity-provider connection options.
Before SAML testing, Atlassian recommends HTTPS between the IdP and app, synchronizing the IdP server clock with NTP because SAML requests have limited validity, and planning downtime for setup and testing. Prepare a test authentication policy and a test user. Also identify who can recover access if a policy or configuration prevents ordinary sign-in.
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Configure SAML SSO and enforce it gradually
- Configure the IdP connection. In Atlassian Administration, follow the SAML setup flow for your selected identity provider and save the configuration. Use the provider-specific Atlassian instructions rather than assuming every IdP uses identical fields or steps. For Microsoft Entra, see Microsoft’s Atlassian Cloud SSO tutorial.
- Create a limited authentication policy. After configuring SAML, enforce it through an Atlassian authentication policy. Start with a test policy and a small, selected group rather than applying it organization-wide.
- Verify sign-in before expanding. Test successful sign-in and resolve errors with the IdP and Atlassian configuration before adding more users. Users included in an enforced SSO policy who cannot authenticate through that IdP may be unable to sign in; use a separate policy where appropriate for accounts that should not be routed through it. Review Atlassian authentication policy settings.
For one organization using multiple identity providers, Atlassian’s connection guidance says an Enterprise plan is required. Check plan eligibility before designing a multi-provider or complex multi-domain rollout.
Set up SCIM and validate a small sync
- Configure provisioning in the IdP directory. Follow Atlassian’s instructions for your provider. Securely store the SCIM base URL and API key: Atlassian says these values will not be shown again after setup. Check the key’s expiration date.
- Start with test identities and groups. Create test accounts and groups and review the first synchronization before expanding it. Confirm that account attributes and group memberships arrive as expected, and check the effect on existing users’ access.
- Assign app access deliberately. Grant the synchronized users or groups access to the relevant Atlassian apps. Group synchronization is documented for Jira app instances and Confluence, not Bitbucket or Trello; do not assume group membership is synchronized or grants access in those products.
- Maintain the credential. Atlassian says SCIM API keys newly set up or regenerated beginning in early January 2025 expire after one year. That change did not apply retroactively to keys that already existed. Track the key and its expiration so you can rotate it before provisioning stops.
Use Atlassian’s user-provisioning instructions for the current provider-specific setup and supported behavior.
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Apply Conditional Access in your identity provider
For Microsoft Entra
Configure the Atlassian Cloud enterprise application and scope Conditional Access policies to the intended users and application. Decide which conditions should trigger which controls—for example, requiring MFA, requiring a compliant device, or blocking access. Microsoft notes that multiple Conditional Access policies can apply to a user at once and all applicable policies must be satisfied. Review Microsoft’s Conditional Access policy overview.
Validate policy impact in report-only mode before enforcing it. Microsoft also recommends excluding emergency-access accounts from device-compliance policies; see its device-compliance policy guidance. Keep the Entra policy rollout separate from Atlassian’s SSO enforcement rollout so a failure in one layer is easier to isolate.
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For other identity providers
Use that provider’s official access-policy documentation and its own testing mode, if available. Do not copy Entra-specific policy instructions as if they applied to another IdP. In all cases, scope policies intentionally: an overly broad condition or control can interrupt legitimate sign-in.
Choose the setup that matches your lifecycle needs
| Approach | When it fits | What to account for |
|---|---|---|
| SAML SSO only | You need centralized sign-in and handle account lifecycle changes elsewhere. | Enabling SSO does not also provision, update, or deactivate accounts. See Atlassian’s connection options. |
| SAML plus SCIM | You need centralized authentication and automated lifecycle changes. | Confirm Guard plan requirements, supported group-sync scope, app-access assignments, credential handling, and staged testing. See Atlassian’s SAML and SCIM setup guides. |
| SAML with just-in-time (JIT) provisioning | You want an account created at its first successful SAML login. | Atlassian’s documented prerequisites include linked domains and SSO enforcement on the default authentication policy. Consider SCIM if you do not want SSO enforced on that default policy. See Atlassian’s JIT provisioning guidance. |
| Google Workspace direct integration | Your organization uses Google Workspace for relevant identity functions. | Validate the exact app and organization requirements; group categorization may not be reflected in the same way. See Atlassian’s organization security guidance. |
| Microsoft Entra integration | Entra is your identity provider, and you need its SSO and access-policy controls. | Plan SAML, any needed provisioning, policy scope, and MFA or device requirements against your tenant’s capabilities. See Microsoft’s Atlassian Cloud integration tutorial. |
Keep the rollout recoverable
- Keep SSO enforcement limited until test users can sign in reliably.
- Test provisioning with a small set of users and groups before the first broad sync, then verify app access as well as directory attributes.
- Retain an appropriate administrative recovery path and avoid applying policies to accounts that must remain available for emergency access.
- Expand one control at a time. If sign-in fails, distinguish an Atlassian authentication-policy issue from an IdP Conditional Access denial or a provisioning/app-access issue.
Atlassian’s SAML guidance and Microsoft’s Conditional Access overview provide the provider-specific configuration details.
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