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You’re an employee of the Ltd Co, presuming you’re a director of that company you can pay yourself whatever salary you like - if the Ltd company has funds.
If you are sick/on holiday the Ltd company won’t be invoicing for those days (if the contract is for days worked). Pensions are more complicated and need an accountant to explain.
FTC invoicing through a Ltd Co. Are you eligible for sick/holiday pay and pension or do you need to be PAYE for those?