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File a CIS return in QuickBooks

by Intuit•15• Updated 2 weeks ago

Learn how to file your monthly CIS (Construction Industry Scheme) return directly to HMRC in QuickBooks Online.

From the CIS section, you can file CIS returns, set CIS filing reminders, and track payments invoiced by your subcontractors. To submit CIS for contractors, this would be done via an Employer Payment Summary (EPS) as part of payroll.


Before you begin

Make sure the following CIS information is correct in your Account and settings.

  • Unique Taxpayer Reference (UTR) number  
  • Employer’s PAYE reference number
  • Accounts Office (AO) reference number

File a CIS return to HMRC

  1. Follow this link to complete the steps in product Open this link in a new window
  2. Select CIS.
  3. Select File return for the period you wish to submit to HMRC.
  4. Check that your details in the return are correct and complete, then read the declaration and tick the box to agree.
  5. Then Submit to HMRC.
  6. You'll be prompted to enter your Government Gateway user ID and password.
  7. Select Sign in and submit. QuickBooks will begin connecting to HMRC. This usually takes around 60 seconds, wait until you see a confirmation saying your return has been submitted.
  8. Once HMRC accepts your submission, close the message to return to your QuickBooks.

Once you have filed a CIS return, your next step is to record CIS payments made to HMRC.


Send CIS subcontractor payment and deduction statements

Once you have submitted your CIS to HMRC or marked it as filed, you will be automatically directed to a new screen where you can send subcontractor payment and deduction statements. This means you can meet your legal requirements efficiently and your subcontractors will receive their statements promptly.

  1. On your file return, select the subcontractors you wish to send a statement to
  2. Select Send Statement
    Tip: Make sure your supplier's email address is correct before sending. In the event that any statements fail to send, an error message will appear alerting you to the issue. You can use the Statement status column to track the status.

Note: The number of subcontractors listed on the statement sending page is limited to 50, so if you have more, you will need to send statements in batches, processing 50 at a time and then moving to the next page.

If you file your CIS return through QuickBooks, you can check the status of your submission on the CIS dashboard. It can take up to 72 hours to update the status on the HMRC portal for returns you submit via QuickBooks. Returns submitted via the HMRC Portal will not update the status in QuickBooks.

There are a few reasons why HMRC might reject your return, here's a list of things to check before you attempt to file again:

  • You may be using the wrong login details. Log into the HMRC website to confirm that your Government Gateway user ID and password are correct.
  • Make sure you're using the right 10-digit Unique Taxpayer Reference (UTR) number.
  • Double check that you're using the correct PAYE Reference number.
  • Check that your suppliers have the correct references and CIS setup:
    • Accounts Office reference number
    • Subcontractor UTR number
    • National Insurance (NI) number
    • Verification number
  • Remove any special characters and additional spaces in the subcontractor/contractor name field. Only use letters A-Z and numbers 0-9.

If you need to, here's how you can unfile a CIS return in QuickBooks. Check out the CIS guide for more help articles.


Set a CIS filing reminder

You can set up automatic reminders in QuickBooks Online to keep track of upcoming filing deadlines. To do this:

  1. Follow this link to complete the steps in product Open this link in a new window
  2. Select CIS.
  3. Select Never miss a filing deadline
  4. Tick the send filing reminder email check box
  5. Choose the appropriate day(s) before deadline
  6. Enter your email
  7. Select Save
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