Question
Jira Align synchronization failures due to certificate chain mismatches
Kavi Sage
0 reputation · 12 Mar 2025, 13:42 UTC
140.7K views1
Loading…
0 reputation · 12 Mar 2025, 13:42 UTC
Jira Align requires valid SSL/TLS certificates for secure communication with on-premise Jira instances. When utilizing self-signed certificates or those with incomplete CA chaining, the integration layer often reports generic connection errors within the Sync Status dashboard without granular TLS handshake details.
This issue is exacerbated when the Jira Align cloud service fails to resolve the FQDN of instances behind restrictive firewalls or proxies. There is documented uncertainty regarding how the system handles transient DNS timeouts during high-load cycles, often necessitating manual retries of specific sync jobs.
How can administrators access the specific TLS handshake error codes within the Jira Align integration logs? Is there a configuration-based method to import custom root certificates directly into the Jira Align environment to resolve validation errors?
35275 reputation · 12 Mar 2025, 18:40 UTC
Jira Align typically reports TLS failures as generic connection errors in the Sync Status dashboard. To find the specific cause, navigate to Administration > System > Integration Logs. Look for a javax.net.ssl.SSLHandshakeException. A common indicator of a certificate chain mismatch is the error message PKIX path building failed: unable to find valid certification path to requested target.
If the standard logs are insufficient to identify the exact alert code (e.g., handshake_failure (40)), you must increase the logging verbosity. This requires enabling DEBUG logging for the following packages in the system configuration:
jiraalignorg.apache.http.wire (to capture the HTTP wire trace)javax.net.ssl (to capture SSL layer events)Once enabled, trigger a manual sync. The logs will now contain the raw TLS handshake dump, allowing you to identify the exact point of failure in the negotiation.
The method for resolving validation errors depends entirely on your Jira Align deployment model, as there is no single configuration UI for certificate management.
Cloud administrators cannot directly upload custom root certificates to the Jira Align environment. Because the trust store is managed by Atlassian, you have two options:
For self-hosted instances, you must manually add the PEM-encoded root CA to the Java truststore used by the application. Use the following command as a root/administrator user:
keytool -import -alias internal-ca -file rootca.pem -keystore $JAVA_HOME/lib/security/cacertsAfter importing the certificate, you must restart the Jira Align application for the changes to take effect. Alternatively, you can specify a custom truststore via the -Djavax.net.ssl.trustStore JVM argument.
To verify the fix, run a test sync and confirm the SSLHandshakeException no longer appears in the Integration Logs. Caution: If you enabled DEBUG logging for org.apache.http.wire, revert the log levels to default immediately after troubleshooting to prevent disk exhaustion and avoid logging sensitive data.
Diagnostic Note: Please specify if you are using a proxy or load balancer between Jira Align and your Jira instance, as this may shift the TLS termination point and change where the certificate must be installed.
Use comments to ask for clarification. Post a solution as an answer.
35,275 reputation · 12 Mar 2025, 23:49 UTC
While the integration logs provide high-level Java exceptions, they often don't reveal if the on-premise server is failing to send the intermediate certificates. A common cause of PKIX path building failed is a server that provides only the leaf certificate, relying on the client to have the intermediate CA already cached.
To verify if your Jira instance or reverse proxy is serving the full chain, run the following command from an external network:
openssl s_client -connect <your-jira-fqdn>:443 -servername <your-jira-fqdn>Check the Certificate chain section of the output. If you only see s: /CN=... (the server certificate) without subsequent i: /CN=... entries for the intermediate CAs, the chain is incomplete. Resolving this on the server side—by bundling the leaf and intermediate certificates into a single chain file—often fixes the synchronization failure without requiring Atlassian to manually update their cloud trust store.