I registered a client for PAYEE, in order to get an employer's PAYE number, to then register for CIS as a contractor. The CIS side is all set up and working fine, but now he has the PAYE on his online business account - with no employees. Do i need to now deregister from PAYE so that HMRC are not expecting any monthly returns?
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It depends on what you said when you applied for a PAYE scheme. If you specified 0 employees, but that you were engaging sub-contractors, HMRC should have set up an XP PAYE scheme, under which no RTI returns are required for employees.
If you think you have a PSC scheme for both employees and sub-contractors, I would suggest that you write to HMRC, NIC & EO, BX9 1BX, and ask them to change it to an XP scheme.