I'm not able to get IGST on my invoice for a customer in a SEZ. I've set the GST registration type as SEZ. I still get CGST and SGST.

Hi there, @VG05.

Thanks for stopping by the Community, I'm happy to help you with handling taxes. 

First off, QuickBooks will presume that the transactions are intrastate if a GSTIN is not specified in Tax Settings, and will simply show GST rates.

If the Customer GST Registration Type is Overseas, SEZ, or Deemed Exports, the location of the business is irrelevant. In such circumstances, the sales transactions will only reflect IGST rates. 

Let's perform the following steps from this link to create custom tax rate.

When you edit a rate, you must set an effective date from which the new rate must be effective. This means that the new rate will only be available for new transactions entered after the Effective date. 

You can check this link for more details about editing tax rate in QuickBooks Online.

Please let me know how that works for you. I'll be here if you need more assistance with recording taxes.