I have just set up a new employee who started 2 Sept 2019 and this is the first payroll run he is included in. Tax code is 1250L but no income tax is being deducted.

Hi @rod9,

Let me share some insights as to why the first payroll of your recently added employee doesn't include an income tax.

1250L is a cumulative tax code, which means that if you return to work after a break or if you start working part-way through the tax year, your tax-free personal allowance will have been building up and you may pay less tax for a while. Also, calculations in QuickBooks Online follow HMRC guidelines.

If you'd like a second opinion on your employee's income tax calculation, you can contact an accountant or HMRC for assistance.

You can view this article to become familiar with Payroll Tax Year Changes 2019/2020. Changes such as the increase in auto-enrolment and the auto-enrolment thresholds are listed.

I'll be around in case you have other questions in mind.I'll be sure to get back to you.