Can we raise invoices from multiple branches with different GSTINs

We're unable to create invoices with different GSTINs, Accounts491. I will provide you with some tax information.

QuickBooks can only support one GSTIN per company or account. You'll have to create multiple companies to manage the different tax numbers. Feel free to visit our website and select the plan that suits your business needs. 

Let me add this reference to help you learn more about GST: Setting up QuickBooks for GST.

If you have additional tax questions, don't hesitate to leave a comment below. We'll get back to you as soon as we can. Take care!

@accounts491 

You should have multi QBO accounts to do so.

https://quickbooks.grsm.io/India

Otherwise, consider switching to QB Desktop with a one time license to manage multi company files. Deploy a private cloud if required.