Microsoft Entra ID + Atlassian (Jira + Confluence) integration
Set up Microsoft Entra ID as the identity provider for Atlassian (Jira + Confluence) via SAML + SCIM — via Atlassian Access for Entra-managed users.
- Entra ID Application Administrator
- Atlassian Access subscription
- Atlassian organization admin
1. Create a new SAML 2.0 application in Entra ID
In the Entra ID admin console, create a new SAML 2.0 application. Choose "Web Application" type. Note the placeholders for ACS URL + Entity ID — you'll get these from Atlassian in step 3.
2. Get the SAML metadata URL from Entra ID
Entra ID exposes the IdP metadata at a stable URL. Copy this URL — you'll paste it into Atlassian's SSO configuration. Alternatively, download the metadata XML if Atlassian doesn't support URL-based metadata.
3. Configure SSO in Atlassian
In Atlassian's admin → security → SSO settings, paste the Entra ID metadata URL (or upload the XML). Atlassian will display the ACS URL + Entity ID it expects — copy these.
4. Return to Entra ID + complete the SAML app config
Paste Atlassian's ACS URL into the Entra ID app's Single Sign-On URL field. Paste the Entity ID into the Audience URI field. Set the NameID format to EmailAddress (or persistent if Atlassian expects that).
5. Configure attribute mapping
Map the attributes the SP expects (see the Attribute Mapping section below). At minimum, email is required. Most apps also expect firstName + lastName.
6. Assign users + groups
In Entra ID, assign the SAML app to users or groups that should have access. Test with a pilot group before broad rollout.
7. Test end-to-end
Sign in to Atlassian via the IdP-initiated link (from Entra ID dashboard) AND via SP-initiated (direct Atlassian login URL). Both should work. Check the SAML Tracer browser extension or SAML decoder to inspect the assertion if anything fails.
What flows from where.
| Source (Microsoft Entra ID) | Target (Atlassian (Jira + Confluence)) | Note |
|---|---|---|
| user.mail | NameID | — |
| user.mail | — | |
| user.displayName | name | — |
- Clock skew: Entra ID and Atlassian clocks must be within ~5 minutes. NTP-sync both. SAML's NotBefore + NotOnOrAfter are strict.
- NameID format mismatches are the most common failure. Atlassian typically wants EmailAddress; Entra ID defaults vary. Mismatch → cryptic "invalid assertion" errors.
- Just-in-time (JIT) provisioning vs SCIM: many apps support both. SAML JIT creates the user on first SSO; SCIM creates them ahead of time. Pick one — both can cause attribute drift.
- Audience restriction: Atlassian's expected Audience URI must match exactly what the IdP sends. Trailing slashes + protocol (http vs https) matter.
- Signed Response vs signed Assertion: many SPs require the Assertion to be signed (not just the Response envelope). Check the SP's docs.
- Atlassian Access required — the org subscription, not per-product.
- Entra ID provisioning to Atlassian goes via SCIM; some custom attributes don't round-trip cleanly.
- IdP-initiated SSO works (sign in from the IdP dashboard)
- SP-initiated SSO works (visit Atlassian directly + get redirected to IdP)
- User attributes flow through correctly (email, name, groups)
- Logout (single logout if supported) works as expected
- Step-up MFA fires when policy requires it
- Unauthorized users (not assigned to the app) get a clean denied message
- Capture a successful SAML response and inspect it (use the SAML decoder tool)
For the latest vendor-side configuration changes, refer to:
Entra ID + Atlassian →