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Currently using FreshDesk to track requests and tickets internally and another team within our company is also looking to hop onboard to also use. The agents would be completely separate from my team, and would want their tickets to also be separate. 

Would my best option be to create a new Group and set up automations that way or have them set up a new FreshDesk scenario, so their “desk” is completely separate from mine? Or is there an option C that I am not aware of that could also solve this issue?

If you just need to keep tickets and agents separate but still manage everything in one place, creating a new Group with routing rules works well. If you want full isolation (settings, reporting, and data), then a separate Freshdesk account is the better choice.

There’s also a middle ground: if your plan supports it, you can use Freshdesk’s Multiple Products feature — this lets each team have its own “desk” but still under one account.

It really depends on whether you want shared visibility or complete separation.