I registered late for employment allowance, it has now been submitted. But when I run payroll it is still deducting employers national insurance?

 Thanks for joining the Community, @MINERSLAMP 

Does the amount appear on the P32 under EMP? This means that is has been used and deducted against the employer's NI allowance for this tax year. 

If you need any further guidance, please get back to us below with the version of QuickBooks Online payroll that you're using (Standard/Core or Advanced). 

We are using payroll standard. We have not used our employment allowance for the year but when I run payroll it adds employers NI. Should I not pay the employers NI and let it sort itself out in the year end payroll?

I registered us for EA today and it has been accepted but when I checked our HMRC PAYE account online it says we are not registered. When the account is updated will that allow me to run payroll without ENI?

Hi there, @MINERSLAMP.

Let me share info about registering for Employment Allowance and running payroll without EIN.

The Employment Allowance (EA) has guidelines for you to be registered. So, before you set up the EA, ensure you're eligible. See if you qualify on the HMRC website. Or, if you're not sure of your eligibility, read the employer guidance. 

Moreover, you need to register as an employer with HMRC to receive your PAYE reference number, Accounts Office reference number, Government Gateway user ID, and password. Feel free to read this article for more info: How to run payroll in QuickBooks Online Payroll.

The Employer's Identification Number (EIN) is from the US. While, the equivalent for this in the UK is a Unique Tax Reference, which is a ten-digit number assigned by HM Revenue and Custome (HMRC). And to answer your question, yes, you can still run payroll without this.

To help you prepare for the year-end tax, check out this article: Year-end guide for QuickBooks Online Standard Payroll.

If you have further questions about EA and running payroll, click the reply button below. I'll be willing to lend a hand. Keep safe and have a good one.