Paying emergency tax but won’t earn over the Personal Allowance threshold

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Hi, I’m hoping someone can help me as neither of the HMRC helplines or Google seem to be able to help.

I operate as director of a limited company but am paying myself up to the Personal Allowance this tax year as salary with the rest as dividends so as an employee won’t personally owe any income tax or NI.

I used the HMRC basic PAYE tool to submit my first months salary in December which calculated income tax and ni payable by the business on behalf of the employee - this is incorrect as I haven’t used my PA yet but the software wouldn’t allow me to amend it.
I ensured to update (personal) HMRC of my expected salary and received my updated personal tax code, which I have submitted to the HMRC software.

HMRC are still requiring the business to pay the tax and ni they have calculated by this months deadline (22nd). I have rung HMRC helpline to see if they could amend something to stop the payment coming out of the business only to be reclaimed following the p800, they directed me to the technical HMRC helpline, who also haven’t seemed able to amend the incorrect calculation in the software so it still seems the business has to pay the income tax/ni for me personally to wait for a refund.

1. Has anyone had this happen and know how I can avoid ultimately loaning HMRC my money for a bit?
2. If not and I end up paying c. 2.5k in tax this tax year, how do I treat a refund? Am I best to pay myself a salary of PA-2.5k and then can I declare the refund as the rest of the salary in this tax year (regardless of when physically received)? or as it will probably be paid next tax year does it have to be paid then in which case I can balance it off next years salary? 

I appreciate a tax refund isn’t salary but any earnings over PA I will pay myself as dividends so trying to avoid any income over PA which will be liable for tax+ni.

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  • tacpot12
    tacpot12 Posts: 7,973 Forumite
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    Have you discuss this with your accountant? Your accountant should have told you how to avoid this problem in the first place. 
    The comments I post are my personal opinion. While I try to check everything is correct before posting, I can and do make mistakes, so always try to check official information sources before relying on my posts.
  • penners324
    penners324 Posts: 2,741 Forumite
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    If you've submitted the rti then you'll have to pay it.

    Then update your tax code in the paye tool and it will reclaim it in January 
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