I have been paying tax and NI contributions as a self-employed person, albeit only a tiny bit of tax as I earn just over the allowance threshold. I have now taken on additional regular work to supplement my self-employment income on a PAYE basis. The employer has asked for a P45, which I do not have, and am paying tax and NI on an emergency code. Do I have to wait until my year end 2016/2017 accounts have been processed at the tax office to get back any over payment in tax and NI contributions?
A P45 is only provided by an employer upon cessation of your employment with them. As you were self-employed you obviously aren't eligible for a P45.
In this scenario you will need to complete a starter checklist (previously referred to as a P46) and select the statement that reflects your circumstances the best (probably statement 'C')
Now that employers are using Real Time Information (RTI) reporting, you can also phone HMRC after your first pay day and ask them to correct your records from their side (make sure you have your NI Number, Payroll ID and Employer's PAYE Reference to hand). They will then send an electronic coding notice to your employer and advise them which tax code to use going forward.
If you are placed on a cumulative tax code (doubtful in this scenario) then your tax will correct itself and you won't need to do anything further. If you are given a non-cumulative tax code then you will need to complete a self-assessment at the end of the tax year using your P60 certificate - this will be issued by your employer at Tax Year-End (TYE) assuming you are still an active employee as at the 5th April. If you leave employment before the 5th April then your employer will issue you a P45 which can be used instead for your self-assessment.