Quick answer
If you’re a self-employed subcontractor under the Construction Industry Scheme, your qualifying income is your gross payments before CIS deductions and before expenses. The tax your contractors deduct still counts as tax paid towards your bill, and you claim it in your final declaration.
Gross, not net
If contractors paid you £45,000 for your labour and deducted £9,000 under CIS, your turnover is £45,000, not the £36,000 you received.
What to record
The gross amount of each payment
The CIS deduction shown on each payment and deduction statement
Materials and other expenses
Getting CIS deductions back
CIS deductions are tax paid on account. You include the total in your final declaration, and it’s set against your tax bill.
See MTD for sole traders for the general rules.