If you pay CIS deductions, you can claim this back through your company’s payroll. If you use Clear Books Payroll, the EPS form will be automatically updated with any CIS deductions from paid sales invoices.
This guide demonstrates how a CIS deduction on an invoice affects the EPS form and how to submit the EPS via Clear Books Payroll.
For further information from HMRC please see their guidance below:
If you submit a Self Assessment tax return, you can use the CIS suffered report on the Tax > CIS > Suffered report to find all paid invoices with CIS deductions.
Ensure that your CIS sales invoices have their payment allocated to them. The CIS deduction will not occur in the File EPS in the Payroll module until this has happened.
Navigate to the Payroll module by clicking on the link along the top navigation bar.
Go to Employer > RTI > File EPS. This will take you to the RTI EPS form which needs to be submitted to HMRC.
Check the figure under the YTD CIS deductions from payments that they match the amount in your sales CIS.
Click on the Send to HMRC button at the bottom.