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Level 1

CIS deduction issue with QBO

Hi, new to quickbooks and to the community so sorry in advance if I'm being dense, and for the below word salad... Which hopefully makes sense. 


I signed up for an account today and I think I've been a bit misled, either that or I'm not using the software correctly.


I'm a sole trader in the construction industry. I mainly work for a couple of contractors or on my own private work. I never, ever, employ other people myself. 


However, the contractors I work for are obviously CIS registered. I invoice them with my total amount, they then deduct for CIS and pay me the correct amount.


I explained this very clearly to a quickbooks advisor on the phone. They told me to get the QBO plan and not the SE plan as the latter doesn't include CIS. 


Having looked through, the CIS section solely deals with payroll/employees etc. It has seemingly no capability the other way round.. Ie, accounting for CIS deductions made by the person you're sending the invoice to.


On the otherhand, if I had signed up for the standard SE plan and sent my gross invoices to the companies I work for... When they pay me less than the invoiced amount (because they've taken CIS at source), it'll throw my books off completely, no?!


So I feel like I've been up-sold a product I didn't need (and I can't revert down anyway) and the SE version wouldn't work for what I actually need.


Surely this is pretty common though, and there should be a way for it to work with either QBSE or QBO or another accounting software?? 

QuickBooks Team

CIS deduction issue with QBO

Hello, @Knotwerx. Thank you for raising your concern here in the QuickBooks Community.


I'm happy to provide insights about the Construction Industry Scheme (CIS) feature in QuickBooks.


Currently, this feature is only available in QuickBooks Online subscriptions and not in QuickBooks Self-Employed. If you want to calculate your CIS deductions, track CIS withheld or suffered amounts, and generate the necessary reports for HMRC, I highly recommend subscribing to QBO. 


To view which product is the best suited for your business, you can check out our Plans & Pricing page.


When you turn on CIS, QBO creates the relevant accounts in your chart of accounts. These accounts will be used to calculate CIS on your transactions and map to your CIS reports, allowing you to easily track the CIS withheld.


Please note that even if CIS is more likely to deal with payroll, you'll need to create an invoice or sales receipt to track your CIS transactions in QuickBooks.

For additional reference, you can check out these resources:



Please don't hesitate to comment below if you have other concerns about the CIS scheme in QuickBooks. I'll gladly help. Keep safe, and I wish you continued success.

Level 1

CIS deduction issue with QBO



Thank you for the reply. The problem is I can't use any of the CIS functions because it requires you to input a Paye reference number and an accounts office reference number.... Neither of which I have because I don't employ anyone, as I carefully explained to your sales colleague. 

QuickBooks Team

CIS deduction issue with QBO

Hi Knotwerx, thanks for getting back to us here. If you don't have an Employer’s PAYE reference no. or Accounts Office reference no. you can leave these fields blank or enter dummy information to access the CIS feature. Information entered here isn't submitted to HRMC, however, you would need to request this if you need to submit CIS filings from QuickBooks. 

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