I would like to use Quickbooks to prepare CIS returns but it won't let me as it wants me to file all previous ones but they have already been filed with HMRC

Hello, and welcome to the Community. I appreciate your reaching out to us. I'll provide you with further information regarding the CIS returns in QuickBooks Online.

You have to record the VAT payments you made outside of QuickBooks for it to recognize that they have already been filed with HRMC. Here's how:

To record a VAT payment:

1. Select the Taxes menu, and hit VAT.
2. Click the dropdown menu next to the return.
3. Hit Record Payment, then select the bank account you've used to pay HMRC.
4. Type in the payment date and amount in the appropriate fields.
5. Click Save.

For more details, check out this article: Record a VAT payment or refund in QuickBooks Online.

You may want to review these articles in managing your VAT in QuickBooks Online:

• Make VAT adjustments in QuickBooks Online
• File your VAT return and record tax payments in QuickBooks Online

Please don't hesitate to click the Reply button below if you need assistance with any QuickBooks-related concerns. I'm always here to help you. Have a wonderful day.