I ran Month 3 Payroll and realised I need to turn on Employment Allowance. Done it and logged into my PAYE online for employers account but have to pay NI from Month 2.

We're unable to backdate the Employment Allowance you've turned on after running your month three payroll, sirajmahmood499. I'll provide more details below.

Since you're no longer required to submit the Employer Payment Summary (EPS) for month two where you paid the National Insurance (NI), you'll want to notify or reach out to HMRC through their Basic PAYE Tool. This way, they'll be able to assist you further with the payroll tasks including the management of taxes and NI deducted from your employees' pay.

 Please don't hesitate to get back here in the Community space if you have more queries about managing your payroll tasks in QuickBooks Online, We're always here to help, sirajmahmood499.