Troubleshooting a pay run

The first thing to know

While a pay run is in draft or calculated state, you can re-calculate freely. Each calculation reads the latest employee data and refreshes the numbers. Only finalised runs are locked.

So when something looks off:

1. Fix the underlying data (tax code, salary, sacrifice arrangement, etc.)
2. Click Calculate again
3. Review

Common issues and what to check

Income tax shows £0 for an employee

• They have no tax code set. Open their detail page > Employment > Tax codes and add one.
• Their tax code is NT (no tax). Confirm this is intentional.
• They're on a W1 or M1 code and earned less than the period personal allowance this period. Expected behaviour.
• They're on a cumulative code, and previous over-tax in the year is now refunding. Expected behaviour.

NI shows £0 for an employee

• They're on category C (over State Pension age or director paid only above the threshold). Check this is intentional.
• Their earnings are below the Primary Threshold for this period. Expected.
• They're a director on the annual cumulative method, and cumulative earnings haven't crossed a band yet. Expected behaviour early in the year — NI catches up later.

Negative net pay

• A salary sacrifice arrangement exceeds gross pay. Reduce or end the arrangement and re-calculate.
• A statutory absence is replacing all earnings, but pension contribution still applies. Check the pension setup.

Net pay doesn't match last month

• A tax code changed during the year — the cumulative method recalibrates.
• A salary sacrifice was added — reduces taxable and niable pay.
• A statutory absence opened — replaces part of basic pay with statutory pay.
• A bonus or one-off payment was added in the previous month, now ended.

Year-to-date totals look wrong

• A tax code changed mid-year. Verify the history on the employee detail page.
• A mid-year hire's P45 year-to-date wasn't recorded. If you've just spotted this, contact support and we can correct it.
• Previous runs weren't finalised. Only finalised runs contribute to year-to-date.

An employee is missing from the run

• Their contract's end date is before the run's pay period. They were terminated before this period.
• Their start date is after the run's pay period. They join next period.
• They were hired but no contract was created. Open their detail page > Contracts tab; if empty, contact support.

Still stuck?

If you've checked the obvious causes and the numbers still don't make sense, click Calculate one more time to be sure you're looking at fresh figures, then email support@blankitt.com with:

• The pay run period and payment date
• The employee(s) showing wrong numbers
• What you expected
• What the run currently shows

We'll look at the calculation steps and tell you which input is producing the unexpected output.

Once you're happy

When the figures match your expectation, click Finalise. The run becomes read-only, year-to-date totals lock in, payslips become available, and export to Xero / Sage / BrightPay is enabled.

If you spot an error after finalising, the safe correction is to adjust in the next pay run — same as how HMRC handles RTI corrections. Contact support if you need to fully void and replace.