In order to submit a CIS Return using Quickbooks you will need to follow this step by step guide:

Quickbooks Up To Date

Make sure Quickbooks is up to date - to do this you need to make sure that:

Your bank is reconciled, click here for a tutorial on how to do that.
The outstanding suppliers figure is correct. To view this, go to reports/’accounts payable ageing detail’ to view the outstanding suppliers. If there is a supplier balance that doesn’t look right you’ll need to investigate (i.e. the invoice is dated a while ago, the open balance is negative or the balance seems a lot higher than what you expected).

Add a Bill

Go to Taxes/CIS and you can view the CIS statement that you wish to submit to HMRC. Take a note of the CIS deducted value as you’ll need to enter it as the ‘Amount’ value in our bill below.

Go to the plus sign '+' at the top right of your screen, select bill under suppliers and enter the following information:

Supplier: CIS due
Bill date: CIS Return end date (5 December in our example above)
Category: CIS witheld
Amount: Amount paid to HMRC (i.e. ‘CIS deducted’ value on CIS Return section of Quickbooks)
VAT: No VAT

Click ‘Save & Close’

Reconcile CIS

This section makes sure that everything has been added onto your CIS Returns. If a bill paid to a subbie is for a period before the CIS Return you’re doing and it was added after you completed the previous return it will be missed if you don;t reconcile the CIS withheld account.

Go to the cog at the top right of the screen, under tools click reconcile and enter the following information:

Account: CIS withheld
Ending balance: 0.00
Ending date: CIS Return end date (5 December in our example above)

& then click start reconciling.

You will then need to select the CIS liabilities (charges) that the CIS payment relates to so the difference figure at the top right of your screen is £0.00. Once it does equal 0.00, click ‘finish now’.

Submit CIS Return

Go to Taxes/CIS and you can view the CIS statement that you wish to submit to HMRC.

Login to HMRC's government gateway by clicking here. You'll then need to enter the following details into your CIS Return:-

Total Payments
Cost of Materials
CIS Deducted

Pay CIS to HMRC

Your CIS is due to HMRC two weeks after the CIS Return end date. For example, a CIS Return dated 5 December would be due 14 days after this date which would be the 19th December. To pay you can use the following link:-

www.tax.service.gov.uk/pay-online/epaye

You will need your accounts office reference number which you should have received via letter from HMRC.