New Jira site is automatically linked to existing organization – how to create a fully separate one?

[Yvonne Miglar]

Hi ,

I’m currently trying to set up a second Jira Cloud environment for a separate company, and I’m running into an issue with how Atlassian handles organizations and billing.

Here’s my situation:

• I already have an existing Jira setup under one company
• I now want to create a completely separate environment for another company (different legal entity, different country, different billing details)
• I created a new Jira site using my existing user (name@company.ch)

However, I noticed the following:

• The new site seems to be automatically linked to the existing Atlassian organization
• Billing details are shared or reused, instead of being independent
• I’m also unable to correctly set the country (Germany) for the new setup

My goal is to have:

• A fully separate Atlassian organization
• Completely independent billing profile
• Separate company address and country
• Clear separation between the two companies (no shared administration layer)

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My questions:

1. Is it expected that a new site created with an existing Atlassian account is automatically assigned to the same organization and billing profile?
2. What is the correct way to create a truly separate organization, not linked to the existing one?
3. Would creating the new site with a different email/domain (e.g. name@company.de) solve this? The Domain company.de is verified in the .ch Jira Cloud environement. Does this have an effect? 
4. If a site has already been created with the wrong organization/billing setup, can this be changed afterwards, or is it better to start over?

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Thanks in advance for your help!
I want to make sure I set this up correctly from the beginning, since the environments belong to two completely different companies.

[Martin Runge · Accepted solution]

Hi @Yvonne Miglar

Welcome to the Atlassian Community!

To achieve complete data, billing, and administrative isolation between these two distinct companies, you should use a separate email address (a new Atlassian account) with the targeted company's domain to sign up for the new site.

You can create a new organization also here: https://admin.atlassian.com/o/create 

If you have already created the site and other resources under the wrong organization layer, you can request a specific migration with Atlassian Support to move the site to a newly registered independent organization. You can only move all apps to another organization, so starting fresh again or creating a support ticket is needed.

[Yvonne Miglar]

Hi Martin,

thanks a lot for your helpful explanation – that already clarified quite a bit 👍

I do have a follow-up question regarding the behavior I’m currently seeing, as I’m still unable to create a fully separate organization.

It seems that the email address yvonne.miglar@luartxit.de is already present in the existing .ch organization (luartx.ch), but only in an inactive state (shown as “not invited”) and the account has never actually been used to log in.

However, when I try to create a new organization using this email address, Atlassian consistently redirects me to the existing login flow, including prompts like password reset, instead of letting me complete a clean signup for a new organization.

This leads me to the following questions:

1. Could this behavior be related to the domain verification of the existing luartx.ch organization - the Domain luartxit is verfied there as currently the Users are using this organisation. Or is that unlikely in this case?
2. Does the fact that the user is already present (even if not invited/active) in the existing organization cause Atlassian to treat it as an already managed account?
3. Would you recommend removing this user entry from the current organization first, or is it better to create a completely new Atlassian account (e.g. a fresh admin account under the luartxit.de domain that has never been associated with the existing org)?
4. Alternatively, is there a way to “reset” the association of this email so it can be used for a clean, separate organization setup?

My goal is to ensure a strict separation between two companies, including completely independent organization, billing, and administration layers, so I want to avoid any hidden linkage from the beginning.

Thanks again for your support!

Best regards,
Yvonne

[Martin Runge]

Hi,

Even though the email address ...@luartxit.de is marked as not invited or inactive inside your existing organization, a global Atlassian ID record already exists for it in the background. Because that Atlassian ID exists, the sign-up system blocks a clean, fresh registration flow and routes you into a standard password recovery and sign-in loop for security validation.

This is independent of domain verification, as the system treats any existing email record as a managed account that requires password verification before provisioning the new architecture. To bypass this loop and guarantee an immediate, fully isolated administrative separation, I would highly recommend creating a brand-new (your question #3), unused admin alias under your desired domain that has never interacted with any Atlassian platform service.

[Yvonne Miglar]

Many thanks Martin