I’ve helped dozens of small businesses recover VAT repayments stuck in HMRC’s system, and I know how frustrating it can feel to wait weeks (or months) for money that’s rightfully yours. Below I share a practical, step‑by‑step approach I use with clients at Muressaccounts Co to chase and secure overdue VAT refunds from HMRC without letting the process turn into an accounting headache.

Why VAT refunds get delayed (and what to expect)

Understanding the common reasons for delay helps you focus your chase on the right things. HMRC often holds repayments for reasons such as:

  • Missing or mismatched VAT registration details
  • Inconsistencies between submitted VAT returns and previous returns
  • Random risk-based checks or manual verification
  • Duplicate submissions or refunds already issued to a single VAT registration number
  • Bank details not verified or changed recently

    • Delays are not always a sign of error on your part, but they do mean you need to be organised when you follow up. I always tell clients: keep calm, gather evidence, and follow a clear escalation path.

    Practical checklist to prepare before you contact HMRC

    Before you call, email or use the Government Gateway, make sure you have the essentials at the ready. This speeds up resolution and reduces back-and-forth.

  • VAT registration number and official company name (exactly as HMRC has it).
  • VAT return reference or accounting period relating to the repayment.
  • Amount of repayment and the date the repayment was expected.
  • Bank details on file with HMRC (account name, sort code, account number).
  • Evidence that supports the repayment — e.g., copies of the VAT return, bookkeeping reports from Xero/QuickBooks/FreeAgent, payment screens showing zero bank transfer, and any HMRC letters or notifications.
  • Authorisation proof (if you’re calling for a client): VAT agent authorisation or a client permission letter.

    • Step‑by‑step chase plan I use with clients

    Follow these stages in order — each step builds on the previous so you don’t waste time repeating information.

  • Step 1: Check online first

    • Log into the VAT section of your Government Gateway (or your agent’s HMRC service). HMRC sometimes displays a short note explaining the hold. Also check your bank statement to confirm the payment hasn't arrived under an unexpected descriptor.

  • Step 2: Reconcile your records

    • Pull the VAT return report from your accounting software (Xero, QuickBooks, FreeAgent) and compare it with the submitted return. I often find simple mismatches — e.g., a reversed purchase coded to the wrong VAT box — that explain the hold.

  • Step 3: Call HMRC VAT Helpline with evidence

    • When you call the VAT Helpline (0300 200 3700 in the UK), have your checklist items to hand. Be polite but firm. Ask for a case reference and the specific reason for the hold. If you’re an agent, make sure the agent services PIN or VAT agent details are ready.

  • Step 4: Follow up by secure message or post

    • If the helpline agent promises a review, ask them to confirm the timescale and the case reference by secure message or letter. Follow up with scanned evidence via HMRC’s secure inbox (if available) or by recorded post if documentation is required.

  • Step 5: Escalate if required

    • If you’ve waited the promised timescale without a response, escalate. Ask for a senior advisor or request the case be moved to the VAT compliance team. Be specific — quote dates, amounts and your case reference. Persistence pays here.

    Sample email/message you can send

    Use this as a template when sending evidence through HMRC’s secure message or your client’s agent inbox. Edit the bolded parts.

    Subject Query — VAT repayment for period MM/YY — VAT registration GB123456789
    Body

    Dear HMRC,

    I am contacting you regarding the VAT repayment of £XXXX.XX for the VAT period ending DD/MM/YYYY submitted on DD/MM/YYYY (return reference XXXX). The amount has not been received into our bank account and there is no note explaining the delay on the Government Gateway.

    Attached are: (1) a copy of the submitted VAT return; (2) our bookkeeping report from Xero/QuickBooks/FreeAgent; (3) bank statement showing no incoming HMRC payment; and (4) proof of bank details currently on file with HMRC.

    Please could you confirm the reason for the delay, provide a case reference, and advise the expected timeframe to release the repayment? If further information is required, contact me on 0XXXXXXXXX or reply to this message.

    Kind regards,

    [Your name]
    [Company name]
    VAT reg: GB123456789

    Timescales and what’s realistic

    HMRC aims to process repayments within 10 working days for straightforward claims paid by bank transfer, but in practice you should plan for up to six weeks where verification checks are triggered. If HMRC starts a compliance check that’s more extensive, it can take several months. Track each interaction in a simple spreadsheet so you can point to dates and case references — this often speeds up escalation.

    When you need to involve an agent or a tax adviser

    If you’ve followed the steps above and still have no satisfactory response, consider formally appointing an accountant or VAT agent. Agents can use the Agent Services Account and sometimes get faster, more helpful routing through HMRC. I’ve had clients who resolved stuck repayments within days once an authorised agent intervened — especially where documentation or technical explanation (e.g., treatment of partial exemptions) was needed.

    Practical tips to avoid future delays

  • Keep bank details updated with HMRC and verify them after any change.
  • File returns early where possible — late returns trigger additional checks.
  • Use consistent supplier/customer naming and VAT treatment in your accounting software to reduce mismatches.
  • Consider adding an accountant as an authorised agent for faster resolution.
  • Keep a standard evidence pack ready so you can send everything in one go (returns, ledgers, bank statements).

    • Real examples from practice

    Recently a café client of mine was owed a VAT repayment of £3,200 that didn’t arrive. HMRC had placed a hold because their VAT registration name included “Ltd” but their accounting software used “The”. A quick call, a screenshot of Companies House, and an upload of the corrected return saw the repayment released within ten days. Small mismatches like that are surprisingly common and straightforward to fix.

    If you want, I can draft the exact message for your situation or review the documents you plan to send HMRC. You can find more practical guides and templates on Muressaccounts Co at https://www.muressaccounts.co.uk — I publish step‑by‑step articles specifically for busy small business owners who want to sort their finances without the headache.