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Filing CIS in QuickBooks Online

As of the 25th August you will be able to file your CIS return directly to HMRC, you will not be able to submit earlier CIS returns in QuickBooks Online.

NoteWe have identified that CIS returns submitted through QuickBooks Online will display an inflated value on HMRC, and have temporarily disabled the ability to submit CIS through QuickBooks Online. We will keep you informed as to any further developments.

Please see the section below for further information.

We have identified that HMRC are displaying inflated values based on the total CIS value, rather than the CIS withheld.

For example an Invoice with a value of £100 at 20% will have a deduction of £20, and this is how the return is shown in QuickBooks Online. When submitted to HMRC, you would see a liability of £100 on the CIS Gateway.

What does this mean for you?

If you have submitted a nil CIS return there is no action required.

If you have withheld CIS in your return, please resubmit the values through HMRC’s gateway as soon as possible. If this step is not completed by the 19th, please contact HMRC CIS Helpline on 0300 200 3210 to correct the error on the return.

Your QuickBooks Online company will show the correct amounts, so no adjustments will need to be made.

How to resubmit your CIS return

  1. Log into QuickBooks Online
  2. On the left menu select Taxes
  3. Select CIS at the top of the page
  4. Open the return submitted to HMRC in QuickBooks
  5. Open a new window or tab in your browser
  6. Log into HMRC
  7. Enter the return as displayed in QuickBooks Online to HMRC
  8. Re-submit your return

Please note: The liability can take upto 24 hours to update on the HMRC portal.

As of the 6th August you will be able to file your CIS return directly to HMRC, you will not be able to submit earlier CIS returns in QuickBooks Online.

Before you do make sure that the information in your Account and Settings is correct. To verify please follow these steps:

  1. Go to the gear icon and select Account and Settings.
  2. Go to the Advanced tab and expand the CIS settings by selecting the Construction Industry Scheme (CIS) option.
  3. Verify your UTR no., Employer’s PAYE reference no., and Accounts office reference no.

Once your details have been verified, please follow these steps:

  1. Go to the Left Navigation and under Taxes, select CIS.
  2. Select File Return for the period you wish to submit.
  3. Please verify the return and once fully satisfied, tick the box: I declare that the information on this return is correct and complete. I understand that a false declaration can result in prosecution.
  4. Select the option Submit to HMRC.
  5. At this stage, you will be prompted to enter your HMRC credentials.
  6. Once you have entered your credentials, QuickBooks will begin connecting to HMRC. This usually takes around 60 seconds depending on how busy HMRC are. Please remain on the screen until you receive confirmation that your return has been submitted.
  7. Once you see the message that your return has been accepted by HMRC, you can close the message and return to the main screen.

Note: If you file your CIS return through QuickBooks, you will see the status in QuickBooks Online but not via the HMRC portal. Likewise returns submitted via the HMRC Portal will not update the status in QuickBooks Online.

If you encounter an error please verify that your credentials are correct before attempting to file the return again. If you are unable to continue or need to unfile your return, don’t hesitate to contact our award winning Customer Success team.

Accounting for the Payment made to HMRC

To account for the payment you make to HMRC following a CIS submission:

  1. Go to create an expense.
  2. If you have created a supplier for HMRC, then please enter the name in the supplier field.
  3. Select the bank account from which you have paid HMRC and select the date the payment was made on.
  4. In the table section, under the Account column select the CIS Payments to HMRC account.
  5. Enter the amount you have paid HMRC.
  6. Select Save and Close

Please note that once you have submitted your return in QuickBooks, previous periods including the one you have submitted will be closed. You will not be able to create or edit any CIS transactions in closed periods.

If you do need to create or edit previous transactions you will need to unfile your return. To do so, please contact our award winning Customer Success team.

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