Integrate with Zendesk

[Annie Tay]

Hi!

We are trying to integrate Jira and Zendesk. 

We tried the legacy integration Zendesk Support for Jira which works perfectly but it will be deprecated in April 2026.  We liked the feature where the control/restriction of the project to be seen in Zendesk is managed in Jira. 

We tried the new Zendesk support for Jira v2.0 and the control/restriction of the project to be seen in Zendesk is managed in Zendesk.

We further explored the documentation here https://support.atlassian.com/jira-service-management-cloud/docs/integrate-with-zendesk/#Add-a-Zendesk-Integration but could not locate team's operations page and integrations options. 

Would love to hear from the community how you manage the integration!

[Hari Krishna]

Hi @Annie Tay 

What you’re seeing is actually expected behavior, and you’re not missing anything.

The key difference here is that the legacy “Zendesk Support for Jira” integration and the new Zendesk Support for Jira v2.0 / JSM Zendesk integration are built on completely different models.

In the legacy integration, Jira was the system controlling visibility, which allowed you to decide in Jira which projects should be exposed to Zendesk. That capability does not exist in the newer integration, and Atlassian has confirmed this as a product-level design change rather than a configuration gap.

In the newer setup, the source of truth for ticket creation and visibility is Zendesk. Jira Service Management receives alerts or creates issues based on Zendesk triggers, so project-level filtering is intentionally managed from the Zendesk side using triggers, webhooks, and conditions. Jira-side project restrictions like in the legacy app are not supported.

Regarding the documentation: the “team’s operations page” mentioned there refers to Jira Service Management Operations / Alerting (formerly Opsgenie). This navigation is only visible if:

Opsgenie / JSM Operations is enabled for your site, and

You are part of a team configured for alerting/on-call

If you are using standard Jira Software or JSM without Operations enabled, you will not see that page, which is why the docs don’t match your UI.

In practice, most teams managing the new integration do the following:

Control which Zendesk tickets create Jira issues using Zendesk triggers and conditions (group, form, tags, priority, etc.)

Route tickets to specific Jira projects using separate webhooks or integration endpoints

Use Jira Automation only after issue creation for downstream handling

If Jira-side project visibility control is a hard requirement, the legacy integration remains the only option until deprecation. Otherwise, adopting the new integration means shifting project-level control to Zendesk by design.

Hopefully this clarifies the difference and why the documentation feels misleading in this case.

[Annie Tay]

Hi @Hari Krishna , 

Appreciated the response!  A few further clarifications here:

1. Will Zendesk legacy continue to work after April 2026 - i.e. will it be removed entirely and not usable? Or it will be left as it is and we can still use it without support from Zendesk/Jira?

2. Is it possible to integrate via webhooks or integration endpoints without the app Zendesk Support for Jira v2.0?

Thank you!

[Hari Krishna]

@Annie Tay , Glad it helped

The legacy Zendesk Support for Jira integration is planned to be fully retired after April 2026, not just unsupported. There’s no guarantee it will continue to work beyond that date, so relying on it long term is risky.

Yes, you can integrate Jira and Zendesk without the v2.0 app by using Zendesk triggers/webhooks and Jira REST APIs. This gives you more control, but you’ll need to manage the integration logic yourself and won’t get the out-of-the-box UI features.

If Jira-side project control is a must, a custom webhook/API approach is the best alternative. Otherwise, the v2.0 integration requires managing visibility from Zendesk by design.

[Annie Tay]

I would love to give the custom webhook/api approach (without zendesk app) a try.  I was able to find some documentation but it mainly revolves around the zendesk integration app.  Would you be able to shed some light for suitable documentation for us to dive into?

Separately, how do I find out if I can enable JSM with Operations or not?

[Hari Krishna]

I couldn't find much, just try to follow with the procedure 

For a custom Zendesk → Jira integration without using the Zendesk app, there is no single step-by-step guide. Most teams simply combine a few official docs.

On the Zendesk side, use:

Triggers to decide which tickets should go to Jira

Webhooks to send ticket data

On the Jira side, use:

Jira Cloud REST API to create, update issues, or add comments

https://developer.atlassian.com/cloud/jira/platform/rest/v3/intro/ 

The flow is very straightforward:
Zendesk trigger → webhook → Jira REST API.
Zendesk controls filtering and project routing, and Jira just receives and processes the data.

To check if JSM with Operations (Opsgenie) is available, go to
admin.atlassian.com → Billing → Subscriptions.
If you see Jira Service Management – Operations / Alerting, it’s enabled (or can be enabled). If not, that’s why the “team’s operations page” doesn’t appear in your UI.