How to set up auto-payroll controls to stop duplicate PAYE payments in QuickBooks Payroll

I’ve seen it happen more times than I’d like: a busy business owner or a payroll handler runs payroll, authorises payments, and then—because of a second user click, an unclear bank feed, or a duplicate Direct Debit—HMRC ends up receiving two PAYE payments for the same pay period. It’s an annoying and potentially costly mistake, but the good news is you can put practical, reliable controls in place inside QuickBooks Payroll (and around it) to stop duplicates from happening.

Why duplicate PAYE payments happen (so you can prevent them)

Understanding the root causes makes controls easier to design. From my experience, duplicates usually result from one or more of these:

Two people authorising the same payment without clear ownership of the task.

Manual bank transfers combined with automatic Direct Debits from QuickBooks — both paying HMRC for the same run.

Confusion about payment status because the bank feed hasn’t updated quickly enough.

Rerunning pay and reauthorising payment when the first run actually succeeded.

Incorrect payroll calendar configuration (dates overlapping or repeated pay runs).

Once we’ve pinpointed the likely causes, we can design controls that are small, practical, and repeatable.

Set up clear responsibilities and user permissions

First step: decide who is responsible for payroll from end-to-end. Even if you use an external bookkeeper, there needs to be a single internal owner who checks the bank and confirms payments.

Use QuickBooks online user permissions to limit who can finalise payroll and who can only view payroll reports. I typically recommend only one or two users with “full access” to payroll actions.

Create a payroll SOP (standard operating procedure) that documents who prepares, who reviews, who authorises and who checks bank debits.

Configure QuickBooks Payroll payment settings carefully

QuickBooks Payroll allows setting up HMRC payments via Direct Debit. That’s convenient, but you need to be deliberate:

Enable Direct Debit for HMRC only if you intend to let QuickBooks collect payment. If you prefer to pay manually via bank transfer, disable automatic collection.

Set what QuickBooks calls the “Pay schedule” carefully so pay runs match only one scheduled payment per period.

Review the payroll calendar and ensure pay dates, tax periods and payment due dates are consistent. Avoid multiple overlapping schedules for the same staff.

Use in-app reminders and pre-payment checks

QuickBooks has reminders and alerts. Use them to create a short checklist that must be completed before pressing the final “Submit” or “Pay” button:

Confirm payroll run completed and published.

Check payment method (Direct Debit vs manual BACS) is correct.

Verify bank feed shows sufficient funds and no unexpected pending HMRC debit.

Authoriser signs off (this can be an electronic tick in your SOP).

Reconcile your bank before and after payroll

Bank reconciliation is your safety net. I always recommend reconciling the payroll bank account within 24–48 hours of a payroll run.

Before payroll: clear outstanding items and note any pending Direct Debits for HMRC.

After payroll: confirm the exact value taken and the reference used by HMRC. Most duplicates are spotted here early.

Set up a simple approval workflow outside QuickBooks

Even with tight QuickBooks permissions, having an approval step outside—via email, Teams or a checklist app—reduces accidental repeats.

Example workflow: Payroll processed by Bookkeeper → PDF pay summary uploaded to shared folder → Authoriser confirms via email/teams “Approved for payment” → Responsible person executes payment.

Keep the approval timestamped so you can trace who authorised what and when.

Monitor HMRC payment references and use unique references

When payments go to HMRC, check the reference. QuickBooks typically uses payroll references, but confirm it matches the employer PAYE reference. Mismatched references can look like duplicates to your bank or HMRC.

Maintain a simple log of pay runs and expected amounts and references so it’s quick to cross-check.

What to do if a duplicate payment still happens

Despite controls, mistakes can occur. Here’s my practical sequence of steps to fix it quickly:

Identify both payments in your bank and QuickBooks; note amount, date and HMRC reference.

Check HMRC online payroll account to see how many payments they’ve received for the same period.

Contact HMRC Employer Payment helpline immediately. They can advise on reclaim procedures. Keep call reference numbers.

If the duplicate was caused by your Direct Debit and you want a refund, HMRC can process a refund or set it against future liabilities; ask them for the options and timelines.

Record the duplicate as a temporary suspense entry in QuickBooks (don’t remove either payment until HMRC confirms refund or adjustment). I often use a “HMRC suspense” account so it’s visible on the balance sheet.

When HMRC confirms a refund or offset, record the transaction in QuickBooks and reconcile the bank accordingly.

Use reports and regular audit checks

Run a weekly payroll control report and an HMRC payments report. I recommend at minimum:

Monthly payroll summary report (gross, employer NIC, PAYE, SMP, etc.).

HMRC payment history for the last 6–12 months (compare with bank statement).

Payroll audit log from QuickBooks to see who ran and authorised runs.

Control	Why it works
Single authoriser for payments	Prevents multiple people independently paying same bill
Disable automatic Direct Debit if manual paying	Removes the risk of unplanned automatic collection
Pre-payment checklist	Forces a consistent sign-off and verification
QuickBooks permission restrictions	Limits dangerous actions to trusted staff
Bank reconciliation within 48 hours	Early detection of duplicate debits

Practical templates and next steps

If you want, I can provide a simple payroll pre-payment checklist template you can paste into your payroll folder or into QuickBooks notes. It’s a two-minute checklist that stops most mistakes. I can also walk you through changing Direct Debit settings in QuickBooks Payroll or building a one-person sign-off routine if you’re a very small team.

Setting up these controls doesn’t have to be heavy or formal—small changes consistently applied prevent most duplicate PAYE payments. If you’d like a short walkthrough tailored to your QuickBooks subscription level (Simple Payroll vs Full Payroll) and the bank you use, I’m happy to help with specific steps and screenshots.