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You should have declared the gross amount paid - so daily rate plus expenses and then claimed the expenses arises, to form a true net position.
However, as the end result is the same, there maybe is no harm done, unless you should be registered for VAT, and then this does make a huge difference, as the need to be VAT registered is based on your turnover, so you should consider whether this would put you above £77,000
But I would from now on do it the correct way.And is VAT is an issue, then you will need to rectify this, and your self assessment income and expenditure.
I also have a small concern that as you seem to just work for one contractor that maybe you should have been paid as an employee and not under CIS. But if you have satisfied yourself that you are in fact self employed, and feel sure that this status is correct, inspite of this factor, then all you need to do is address the VAT issue and make sure you declare the income and expenditure correctly from now on.
I have added a link here from the Business Link website - (affiliated now with HMRC) that addresses the issue of whether you should be CIS or PAYE.
Sorry the word contractor usually means within the building industry, so I do apologise for any confusion
Then you are looking like you should be an employee as you work for just one business. And it would not hurt to write to HMRC to state that your annual income was £x and expenses £x but as these are paid back to you, and covered fully, you did not realise that you needed to declare it as total income, less expenses.
But whilst writing I would get clarification that HMRC can view you as a self employed individual, as it does not seem clear cut that you are in fact self employed, as you do not appear to be able to make a loss, are paid all your expenses, so are not even out of pocket with overheads, do not advertise yourself for other businesses to use your skills, which all lean to being employed.