After You File: Refunds, Amendments and Dealing with HMRC (Part 7)

The moment after you submit

Submitting your self assessment return does not end your interaction with HMRC for the year — it begins a new phase. HMRC reviews the return, matches it against data from employers, banks, letting agents and other sources, and either accepts it, queries it, or raises an assessment.

Understanding what each of these outcomes looks like — and what your rights and obligations are in each case — turns the post-filing period from a source of anxiety into a straightforward process.

This is Part 7 of the UK Self Assessment From Scratch series. Parts 1–6 covered whether to file, registration, record-keeping, deadlines, tax calculations, and completing the return. Here we cover everything that happens after the submit button is pressed.

What HMRC does with your return

After you file online, your return goes through HMRC's automated processing system. This involves:

1. Validating the data — checking that all mandatory fields are complete and figures are mathematically consistent.
2. Running the computation — confirming HMRC's tax calculation matches yours.
3. Data matching — comparing what you declared against figures HMRC already holds from third-party reporting (your employer's Real Time Information payroll submissions, bank interest reports, letting agent returns, Companies House director data, Land Registry disposal records, and others).
4. Risk assessment — the system assigns a risk score based on factors like income patterns, expense ratios, previous compliance history, and anomalies between your return and HMRC's data.

Most returns are processed routinely and result in either a tax demand, a refund, or a nil outcome. A small minority are selected for further scrutiny — more on that below.

You can monitor progress by logging in to HMRC Online Services → Self Assessment → View your account. The status will update from "submitted" to "calculation received" as processing completes.

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Refunds: how to get your money back

When a refund arises

A refund occurs when you have paid more tax than the final calculation shows is due. Common reasons:

• You overpaid PAYE during the year (for example, if you left employment partway through the year and your employer used an emergency tax code)
• Your payments on account exceeded the actual tax liability for the year
• You are entitled to relief that was not reflected in your PAYE code (Gift Aid donations, pension contributions)
• You had a loss from self-employment or property that reduces your overall liability

How HMRC pays refunds

The fastest option — always — is to register your bank account in your Personal Tax Account at gov.uk/personal-tax-account. Once HMRC has verified your bank details, all future refunds go by BACS automatically. You can also actively claim a refund there via "Claim a tax refund" rather than waiting for HMRC to process it.

If HMRC holds a credit against your account but you also have a future payment on account due, they may apply the credit towards that POA rather than paying it out. Check your account carefully in this case — the offset will show in your SA statement.

Refund not arrived?

If more than 6 weeks have passed since you filed and no refund has appeared, call 0300 200 3310. Have your UTR and the submission reference number ready. HMRC can trace the refund status and, if it has stalled, re-issue it.

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P800 tax calculations: what they are and when they affect you

A P800 is a letter HMRC sends to PAYE employees and pensioners at the end of the tax year showing their calculation of tax owed or overpaid, based on employer and pension provider reporting.

If you are in self assessment, a P800 should not be issued for the same tax year. Your self assessment return is the definitive calculation for that year, and HMRC processes your position through the SA system, not PAYE reconciliation.

If you receive a P800 relating to a year you have already filed a self assessment return for, contact HMRC (0300 200 3310) to clarify. In most cases, this results from a processing lag where the P800 was generated before your return was matched — HMRC will correct the record.

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Amending a submitted return

Everyone makes mistakes. Perhaps you forgot to include a dividend statement, or you entered a figure from a draft P60 that has since been corrected. The amendment process exists for exactly this.

The 12-month amendment window

You can amend your return online for 12 months after the 31 January filing deadline:

How to amend online

1. Log in to HMRC Online Services
2. Go to Self Assessment
3. Select the relevant tax year
4. Click "Amend return"
5. Navigate to the section containing the error and correct it
6. Work through to the end and resubmit

HMRC recalculates the tax automatically. If the amendment increases your liability, interest (at 7.5%) will accrue on the additional amount from the original payment due date — not the amendment date. If the amendment reduces your liability, HMRC will issue a refund or credit.

Amending older returns

For returns older than the 12-month amendment window, you cannot amend online. Contact HMRC directly — usually by letter to HMRC, Self Assessment, BX9 1AS. Explain the error, the correct figures, and the tax impact. HMRC has discretion to accept corrections under an extra-statutory concession, but this is not guaranteed for very old returns.

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What triggers HMRC to look closer

The vast majority of self assessment returns are processed without further enquiry. A small percentage are selected for additional scrutiny — either through automated risk-scoring or manual review. Common triggers include:

Being selected does not mean HMRC suspects wrongdoing. If your return is accurate and your records are complete, compliance checks are inconvenient but manageable.

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Compliance checks (informal)

An informal compliance check begins when HMRC writes to you asking for information or an explanation. The letter will typically:

• Reference the specific year and return
• Identify the issue (e.g. "Please provide details of the rental income shown on your return")
• Request supporting documents (receipts, bank statements, contracts, invoices)
• Give a deadline for your response (usually 30 days)

Always respond fully and on time. Providing all the requested information promptly, with a clear explanation, resolves most compliance checks by correspondence. Partial responses or missed deadlines signal to HMRC that you are not cooperating, which can escalate to a formal inquiry.

You are entitled to seek professional advice before responding — this is not suspicious and is entirely reasonable. If the query involves complex areas (large capital gains, overseas income, business expense claims), a tax adviser can often resolve the matter more efficiently than self-representation.

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Formal S9A inquiry

A formal inquiry under s9A of the Taxes Management Act 1970 is a more significant step. HMRC opens it by issuing an Enquiry Notice in writing, which must be sent within 12 months of the filing deadline (or 12 months after the return was actually filed, if later).

For the 2025/26 return:

• Filed on 31 January 2027 → inquiry window closes 31 January 2028
• Filed late (say, 15 March 2027) → inquiry window closes 15 March 2028

What a formal inquiry involves

• HMRC has the right to request any documents or information relevant to the return
• The inquiry may be a "full" inquiry (examining the whole return) or an "aspect" inquiry (focused on a specific issue)
• You can ask HMRC whether the inquiry is full or aspect — they are required to tell you
• HMRC sets a timeline and you must respond by deadlines
• If HMRC and the taxpayer cannot agree on the figures, either party can apply to the Tax Tribunal to resolve the dispute

Seek professional representation for any formal s9A inquiry. The stakes include additional tax, interest, and penalties, and the process involves technical legal rights that are worth protecting. Your accountant or tax adviser should attend any meetings with HMRC on your behalf.

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Discovery assessments: HMRC reaching back in time

If HMRC discovers income or gains you did not declare — and the formal inquiry window has already closed — they can still act through a discovery assessment under s29 TMA 1970.

The time limits depend on the taxpayer's behaviour:

These time limits are measured from the end of the tax year — so for 2025/26 (ending 5 April 2026):

• Innocent: HMRC can act until 5 April 2030
• Careless: until 5 April 2032
• Deliberate: until 5 April 2046

This is why maintaining complete and accurate records for at least 5 years (the minimum legal requirement for SA filers) and longer for complex transactions is so important. A property sold in 2025/26 could be the subject of a discovery assessment as late as 2046 if HMRC believes there was a deliberate omission.

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Interest and surcharges on underpayments

If HMRC determines that you owe additional tax — whether through a compliance check, formal inquiry, or discovery — interest and surcharges apply on top of the unpaid tax:

On a £10,000 underpayment held for 12 months, the three surcharges alone total £1,500 — before interest is added. These charges are in addition to any penalty for inaccuracy (which can reach 100% of the tax in cases of deliberate and concealed omissions).

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Your rights when dealing with HMRC

HMRC's Charter (gov.uk/government/publications/your-charter) sets out what taxpayers can expect. Key rights include:

• Right to be treated fairly — HMRC must apply the law consistently
• Right to professional representation — you can have an accountant, tax adviser, or solicitor act for you at any stage
• Right to challenge and appeal — any HMRC decision or assessment can be appealed
• Right to complain — if HMRC handles your case poorly

The appeals process

1. Statutory review: ask HMRC to review their decision internally (usually within 30 days of the decision). A different HMRC officer conducts the review.
2. First-tier Tax Tribunal: if the internal review is unsuccessful or you bypass it, appeal to the independent tribunal. Most self assessment disputes involving sums up to £200,000 are heard at the First-tier Tribunal.
3. Upper Tribunal: further appeal on points of law only.
4. Court of Appeal / Supreme Court: for cases of significant legal principle.

The complaints process

If you have a complaint about how HMRC handled your case (unreasonable delays, rudeness, errors) rather than the tax decision itself:

1. Complain directly to the HMRC office handling your case
2. If not resolved, escalate to HMRC's Complaints team
3. If still not resolved, contact the Adjudicator's Office — an independent body that reviews HMRC complaints

The Adjudicator can award compensation for distress and inconvenience in cases of genuine maladministration.

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What comes next

Part 8 — the final part of this series — addresses the most common self assessment situations and questions that do not fit neatly into a single step of the process: missed deadlines, de-registering, crypto, side hustles, moving abroad, death administration, and more.

Read Part 8: Self Assessment — Answers to the 20 Most Common Questions →