How to deduct a Company Margin fee from an invoice I have set up

Hi there, njowens. To show an admin deduction for a Construction Industry Scheme (CIS) payment on the invoice, you’ll want to ensure the feature is enabled in your account and use the appropriate CIS labour option.

QuickBooks automatically calculates CIS deductions and applies the CIS Suffered amount based on the rate selected, which is then deducted from the total due.

Please note that once this feature is enabled, it can’t be turned off; you can stop using it at any time.

1. Navigate to the Gear icon, then Account and settings.
2. Go to the Advanced tab and scroll down to the Construction Industry Scheme (CIS) section.
3. Switch on the Enable CIS toggle.
4. Enter your company's UTR no., Employer’s PAYE reference no., and Accounts Office reference.
5. You can also tick the I am a CIS subcontractor box if you operate as one, and select your deduction rate from the dropdown menu.

Once enabled, return to your invoice and add a CIS line item. You will see a Less CIS section where you can enter the applicable percentage. QuickBooks will automatically apply the deduction to the invoice total.

After you send the invoice, the reduced amount will be reflected as the final amount due.

However, if the agency is also charging a separate fee, you’d want to create a new service item and record it as a negative line item on the invoice to represent the agency's fee deduction.

If you have further questions, please don't hesitate to click the Reply button below. I'm always here to help.