What Should I Do If HMRC is Chasing Missing PAYE Payments?
Step-by-step process to resolve HMRC payment discrepancies and when we can help with reconciliation
If HMRC is chasing missing payments or you have discrepancies in your HMRC account, don't panic. Here's the step-by-step process to resolve the issue quickly and properly.
⚖️ Important: Your Legal Responsibility
Making HMRC payments is the employer's legal responsibility — not your payroll provider's. We ensure accurate payroll calculations and provide correct payment amounts, but employers must make payments to HMRC on time with proper allocation.
Our role is to:
- Generate accurate payroll reports showing amounts due to HMRC
- Provide the correct 17-digit payment reference in monthly emails (sent on the 6th if you've opted in)
- Ensure our payroll calculations match HMRC's expectations
- Maintain records of what should be paid based on payroll processing
📋 Step-by-Step Resolution Process
Step 1: Check Our Payroll Reports
- Review all payroll reports we've provided for the periods in question
- Verify the amounts due according to our calculations
- Ensure you have the payment schedule for each payroll period
Step 2: Verify Your Payment References
- Always use the exact 17-digit reference from our monthly email (sent on the 6th)
- Never use old references or create your own
- Incorrect references are the most common cause of HMRC allocation problems
Step 3: Review Your HMRC Business Tax Account
- Log into your HMRC Business Tax Account
- Check what payments HMRC has received and how they've been allocated
- Compare this against what you actually sent
Step 4: Make Outstanding Payments
- Pay all amounts shown as due on our reports using HMRC's official payment methods
- Use the correct payment deadlines (22nd of the month following payroll for electronic payments, 19th for cheques)
- Keep records of all payment confirmations
🤝 When We Can Help with Reconciliation
If you've completed the above steps and there's still a discrepancy, raise a support ticket here and we may be able to help reconcile:
- What has been paid against what was due according to our records
- Identify timing differences or allocation errors
- Provide written confirmation of amounts processed through our system
Information we'll need from you:
- Payment amounts made to HMRC and dates sent
- Reference numbers used for each payment
- Copy of any HMRC correspondence
- Screenshots from your HMRC Business Tax Account if possible
⚠️ What We Cannot Do
- Make payments to HMRC on your behalf
- Take responsibility for missed or late payments
- Resolve payment allocation issues directly with HMRC (this requires employer authority)
💡 Preventing Future Payment Issues
Use correct payment references: Always use our provided payment references exactly as written — never modify them or use old ones.
Monitor regularly: Check your HMRC Business Tax Account regularly to spot issues early.
Contact us promptly: If payroll amounts seem incorrect, contact us immediately rather than waiting until HMRC chases payments.
Set up reminders: If you haven't opted in to our monthly payment reminder emails, contact us here to enable them.
📞 Need Help Understanding the Discrepancy?
Payment reconciliation can be complex, especially with multiple payroll periods, timing differences, or allocation errors. We can provide detailed analysis and written confirmation of our payroll calculations to help resolve the issue.
Contact us here with all the information listed above, and we'll work through the reconciliation with you.