Here's how to handle CIS transactions in FreeAgent when you're a subcontractor.
You'll invoice your customers as normal, for the full value of the work done. Don't deduct the tax from this invoice, or your income will be too low.
That means that your customer, the contractor, will pay you less than you invoiced them for. That'll either be 30% less if you're not registered as a subcontractor with HMRC, or 20% less if you are.
Use this method to make sure that your invoices are shown as fully paid.
That depends on your company type.
Explain the payment as Money Paid to User > Drawings, because it's part of your self assessment income tax, which isn't a business cost when you're a sole trader or partner.
Explain the payment as Taxes > PAYE/NI. This is because HMRC set off your CIS deductions against PAYE when your business is a limited company.
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