How do I correct mistakes in quarterly MTD submissions?

Understanding what “quarterly MTD submissions” really mean

Quarterly MTD submissions usually refer to “Making Tax Digital” (MTD) filings that are sent to a tax authority through compatible software on a quarterly cadence. Depending on the regime you are in, “quarterly” might mean updates of income and expenses, VAT returns, or periodic summaries that feed into an end-of-period statement and a final declaration. The common thread is that the information is transmitted digitally and, once submitted, it becomes part of your official record for that period.

That official record aspect is what makes corrections feel intimidating. People worry that “submitted” means “locked forever.” In practice, most systems allow corrections, but the method depends on what you filed, when you filed it, and why it was wrong. Sometimes you correct inside the next submission; sometimes you amend a specific period; sometimes you adjust the end-of-period statement; and in a few cases you contact the authority or your software provider because the issue is not just a number but a fundamental mismatch like duplicate submissions, the wrong taxpayer identifier, or a broken period range.

This article walks you through a careful, repeatable approach to fixing mistakes in quarterly MTD submissions. It aims to help you correct errors with minimal disruption, keep your digital records consistent, and reduce the chance of reintroducing the same mistake later. While the details vary across MTD regimes, the principles—identify, classify, correct appropriately, and document—apply broadly.

Start with a calm audit: what exactly is wrong?

The first step is to identify what is wrong without immediately changing anything. A rushed “fix” can produce a second inconsistency that is harder to unwind. Instead, do a mini-audit:

1) Pin down the submission you believe is incorrect: the quarter, the submission date/time, and the reference number or acknowledgement your software received.

2) Identify the symptom: is the total wrong, are categories misallocated, are transactions missing, are duplicates present, or is the submission attached to the wrong entity or period?

3) Identify the source of truth: bank statements, invoices, receipts, payroll reports, point-of-sale exports, or whatever system generated the numbers. Your goal is to confirm the “correct” position before you decide how to update the “reported” position.

4) Identify the size and nature of the error: an arithmetic error of £50 is treated differently from omitting a month of sales, and both differ from submitting the wrong quarter entirely.

Doing this creates a clean narrative: “Submitted X, should have been Y, difference is Z, caused by A.” That narrative is the foundation of the correction method and your internal compliance notes.

Classify the mistake: the correction method depends on the type

Most quarterly MTD mistakes fall into a few categories. Classifying your error will point you to the right fix.

1) Data entry or categorisation errors

Examples include putting a cost into the wrong expense category, marking a business purchase as private, entering an invoice with the wrong date, or using the wrong VAT treatment (where applicable). These typically do not require you to “cancel” a submission. You correct the underlying transaction and allow the corrected totals to flow through the next update or an amendment process, depending on your regime and software capabilities.

2) Missing transactions

This is one of the most common issues: you forgot to record a sales invoice, missed a supplier bill, or bank feeds failed to import transactions for a week. Missing items often produce a clean corrective path: add the missing transactions to your digital records with the correct dates and supporting documents, then make sure your next submission or amendment reflects the change.

3) Duplicate transactions

Duplicates can happen through bank feed re-imports, repeated CSV uploads, or manual entry followed by automatic sync. Duplicates inflate totals and can make your bookkeeping look messier than it is. The fix is usually to remove or void duplicates in your records (without deleting audit history, if your system uses a soft-delete or void mechanism), then resubmit or adjust according to the rules for your submission type.

4) Wrong period or overlap errors

Sometimes you submitted a quarterly update with the wrong date range (for example, including a month that belonged in the next quarter) or accidentally submitted overlapping periods. Overlap errors can create downstream confusion because subsequent submissions may build on the earlier one. These may require an explicit amendment process or, in some cases, contacting support if the system will not accept a correction due to period constraints.

5) Wrong entity or taxpayer reference

Submitting under the wrong business, VAT number, or taxpayer ID is more serious because the data has been sent to the wrong account. The corrective steps may require you to involve your software provider and the authority, particularly if personal data or another entity’s figures are involved. Do not assume you can “fix it later” purely by adjusting next quarter’s figures if the filing is sitting in the wrong account.

6) Software mapping or integration issues

This includes misconfigured chart-of-accounts mappings, an integration that changed category mappings after an update, or a broken link between your accounting software and an app that supplies data. Fixing the symptom without fixing the mapping often results in the error repeating every quarter. These cases call for extra care: correct the mapping first, then correct the data and submission totals.

Check whether your quarterly submission is “incremental” or “periodic snapshot”

A key concept is whether each quarterly submission represents:

An incremental update (only the activity for that quarter), or

A periodic snapshot (year-to-date totals as of the quarter end, which effectively replaces earlier interim numbers).

This matters because the correction method differs. If your quarterly update is incremental, you may need to file an amendment for that specific quarter or adjust in a later quarter using a deliberate correction entry. If your quarterly update is a snapshot, then correcting your records and submitting the next snapshot may automatically “true up” earlier errors because the year-to-date totals incorporate the corrected data.

Your software’s user interface can give clues: does it ask you to submit “Quarter 1 totals” or “Update to date”? Does it display totals for the period only or cumulative totals? If you are unsure, look at your previous submissions: do the totals increase cumulatively each quarter in a way that suggests a year-to-date approach, or do they reflect standalone quarters?

Even without perfect certainty, you can still proceed safely by correcting your underlying bookkeeping and then choosing the least risky submission approach: either an official amendment if available, or a clear corrective adjustment in the next submission plus documentation.

Before correcting anything: preserve evidence and note what you submitted

It is good practice to capture a record of what was submitted before you change your books. This is not about “keeping secrets”; it is about being able to explain the difference later, especially if you are asked why the numbers changed from quarter to quarter.

Do the following:

• Export or screenshot the submitted totals: income, expenses, VAT elements (if relevant), and any breakdown your software shows.

• Download acknowledgement receipts or submission confirmations.

• Save a copy of the ledger report for the quarter as it existed at submission time if your system supports report locking or “as of” reporting. If not, export the transactions list for that date range and store it securely.

• Write a short correction note: quarter, what went wrong, estimated impact, and likely cause (missing invoices, duplicates, mapping error, etc.).

These artefacts help you, your accountant, and your future self. They also make it easier to demonstrate that the correction is legitimate and not an attempt to obscure earlier reporting.

Correct the underlying records first, not the submission totals

MTD regimes generally expect your digital records to be accurate and to align with what you report. A common mistake is trying to “force” the submission totals to match a desired number through manual adjustments while leaving the underlying transactions wrong. That approach is brittle: the next bank import or reconciliation can undo your forced totals, and you can end up chasing your tail each quarter.

Instead, correct at the transaction level as much as possible:

• If a transaction is missing, add it with the correct date, amount, and category, and attach the source document.

• If a transaction is duplicated, void or delete the duplicate according to best practice in your software (prefer voiding or marking as duplicate if it preserves audit trail).

• If a transaction is miscategorised, recode it and ensure the tax/VAT treatment is correct.

• If dates are wrong, correct the dates so the transaction falls in the right period. Be careful: changing dates changes which quarter the transaction belongs to.

• If a reconciliation error caused misstatements, redo the reconciliation carefully rather than layering adjustments on top.

Once the records are corrected, regenerate your quarter reports and compare the “corrected” totals to the “submitted” totals. The difference tells you how to proceed.

Choose your correction route: amend, adjust next quarter, or correct at year-end

There are three common routes to correcting quarterly MTD mistakes, and you may use more than one depending on the regime and timing.

Route A: Amend the specific quarterly submission

Some systems allow you to amend a previously submitted quarterly update directly (or submit a replacement update for the same period). If that functionality exists and the mistake is material, this is often the cleanest option because it aligns the quarter’s reported numbers with the corrected books.

When to prefer an amendment:

• The error is large enough to distort your understanding of tax/VAT liabilities or business performance.

• The mistake affects a period that is otherwise “closed” and not expected to be corrected through later snapshots.

• You submitted the wrong period range or had an overlap that needs to be fixed explicitly.

Practical steps:

1) Confirm your records are corrected and reconciled.

2) Use your software’s “amend” or “resubmit” feature for the affected quarter, if available.

3) Ensure the amended submission matches the quarter-end totals generated by the corrected records.

4) Save the new acknowledgement and keep both the original and amended confirmations with your correction note.

Route B: Adjust through the next quarterly submission

If direct amendments are not possible (or not necessary), a common approach is to allow the correction to flow into the next quarter’s submission. This works best when quarterly updates are cumulative snapshots. In that scenario, the next submission naturally incorporates the corrected earlier transactions and the tax authority sees an updated year-to-date picture.

When to prefer adjusting in the next quarter:

• The system uses cumulative year-to-date reporting, so the next update will incorporate the corrected data.

• The error is modest and does not require immediate correction of the prior quarter in isolation.

• Amendments are technically possible but would create extra complexity and you have a clear audit trail showing the correction was made promptly.

Practical steps:

1) Correct the underlying records and confirm your year-to-date totals reflect the fix.

2) Make sure your next quarter’s submission uses the corrected dataset (watch for drafts created before you made changes).

3) Maintain a note explaining that “Quarter 2 includes a catch-up correction for Quarter 1” and quantify the net impact.

Route C: Correct at end-of-period / finalisation stage

Some MTD processes treat quarterly updates as informational and rely on an end-of-period statement and final declaration to finalise the tax position. In those cases, certain inaccuracies in quarterly updates may be resolved during year-end adjustments, accruals, capital allowances, and other final entries.

When to prefer year-end correction:

• The error is related to year-end accounting adjustments (accruals, prepayments, depreciation, allowances) that are not meant to be finalised quarterly.

• Quarterly submissions are intentionally “best effort” and you expect the final submission to reconcile everything.

Even here, do not treat quarterly errors casually. You still want your digital records to be correct, and you should correct obvious omissions or duplicates as soon as you detect them. The difference is that you might not need (or be able) to amend the quarter; the finalisation step is where the official tax computation is locked in.

Handling common scenarios with step-by-step fixes

Scenario 1: You forgot a sales invoice in Quarter 2

Symptoms: Reported income is lower than expected; customer statements show an invoice that is not in your books; the VAT or tax totals (if applicable) are understated.

Fix steps:

1) Enter the missing invoice in your accounting system with the correct invoice date and customer details.

2) Attach the invoice PDF or source document if your software supports attachments.

3) If the invoice has been paid, match it to the corresponding bank receipt; if not, ensure accounts receivable is correct.

4) Re-run your quarter report and compare it to what you submitted.

5) Choose the route: if your quarterly updates are cumulative, the next quarter update may correct the year-to-date totals; if not, use an amendment feature if available, or record a correction in the next quarter with an explanatory note.

Scenario 2: A batch of expenses was double-imported

Symptoms: Expenses are unusually high; your bank reconciliation shows duplicate transactions; profit is understated.

Fix steps:

1) Filter your transaction list for duplicates (same date, amount, merchant, and reference). Many tools offer a “duplicate detection” view.

2) Void or delete duplicates according to your software’s best practice. Avoid deleting if it breaks bank feed integrity; instead, mark duplicates as “excluded” or “duplicate” if that preserves the feed while removing the accounting impact.

3) Reconcile your bank account again so each bank transaction is matched once and only once.

4) Re-run reports for the affected quarter and check the corrected totals.

5) Decide whether to amend the affected quarter or let the correction flow into the next update.

Scenario 3: You coded personal spending as business expenses

Symptoms: Certain transactions should be drawings/director’s loan/private, not business; expenses are overstated.

Fix steps:

1) Identify each personal transaction and confirm it is not a legitimate business cost.

2) Recode it to the appropriate private/drawings category so it no longer reduces business profit.

3) If VAT is involved, ensure VAT treatment is corrected too (often personal expenditure is not reclaimable).

4) Add a note on each transaction indicating why it was reclassified.

5) Update the quarter totals by amendment or through the next submission.

Scenario 4: You used the wrong quarter date range

Symptoms: The report includes dates outside the quarter; later quarters show missing months; the submission might overlap with another period.

Fix steps:

1) Determine the correct quarter boundaries and list the out-of-range transactions included/excluded.

2) Correct transaction dates if they were entered incorrectly. If the dates are correct, then the issue is that you generated the submission using the wrong reporting period.

3) If your system allows resubmission or amendment for that period, use it, ensuring the corrected report range matches the quarter exactly.

4) Check subsequent quarter drafts. If they were generated using the wrong starting point, refresh them so they reflect the corrected quarter boundaries.

5) Keep a clear record of what changed and why, because period errors can otherwise look like “moving income around.”

Scenario 5: You submitted under the wrong business account

Symptoms: The submission acknowledgement appears under a different entity in your software; you realise you were logged into the wrong client; the tax authority account shows a filing you don’t recognise.

Fix steps:

1) Stop and do not submit further corrections under either account until you understand the scope.

2) Capture evidence: screenshots of the submission receipt, the account you were in, and the data submitted.

3) Contact your software provider support to confirm what was transmitted and whether they have a formal process for misdirected submissions.

4) Depending on the regime, you may need to contact the tax authority, especially if the submission includes sensitive data or could materially affect liabilities in the wrong account.

5) Once the wrong-submission issue is contained, submit correctly under the right account and document the remediation steps thoroughly.

This scenario is one of the few where “just adjust it next quarter” is not good enough, because the data is in the wrong place.

Materiality: do you need to fix it immediately?

Not every mistake requires the same urgency. A sensible way to prioritise is to consider materiality and risk:

• Financial impact: How much does the error change revenue, expenses, profit, or VAT/tax payable?

• Compliance impact: Does it cause you to miss thresholds, distort liabilities, or break rules around period reporting?

• Repetition risk: Was this a one-off oversight, or is it caused by a process issue that will repeat next quarter?

• Stakeholder impact: Are you relying on these figures for finance applications, investor reporting, or management decisions?

If the error is small and your system’s next quarter update will naturally incorporate the correction, you may choose a lower-friction path. If the error is large, affects the wrong entity, or indicates a systemic mapping problem, you should treat it as urgent and consider amending where possible.

A practical correction workflow you can reuse every quarter

Here is a repeatable workflow that helps you avoid chaos when you discover an issue.

Step 1: Freeze the narrative

Write down what you think happened: “Quarter 3 submission understated income by X because invoices from September were not imported.” This will evolve, but having an initial narrative helps you stay focused.

Step 2: Gather evidence

Export reports, transaction lists, and submission confirmations. If you later need to explain the correction, you will be grateful you did this before making changes.

Step 3: Correct the ledger at transaction level

Add missing transactions, remove duplicates, recode categories, and fix dates. Keep notes inside the system where possible.

Step 4: Reconcile and validate

Reconcile bank accounts, verify control totals (for example, total bank inflows compared to recorded sales receipts over the quarter), and ensure your corrected quarter aligns with reality.

Step 5: Decide the submission correction route

If you can amend and it is appropriate, amend. If not, ensure the next submission reflects the corrected figures and that you can explain the movement between quarters.

Step 6: Document the correction

Keep a short “correction memo” per quarter: what changed, why, how it was fixed, and the net effect on key totals.

Step 7: Prevent recurrence

Fix the process issue: bank feed rules, import routines, cut-off checklist, invoice numbering checks, or staff training.

How to avoid making the correction worse

When correcting MTD submissions, certain traps can create bigger problems than the original mistake.

Trap 1: Changing dates to force a quarter to “look right”

Dates should reflect the real transaction date or tax point rules applicable to your regime, not the quarter you wish it appeared in. If you move dates purely to shift totals between quarters, you risk creating a misleading record and future reconciliation headaches. Correct dates only when they were entered incorrectly.

Trap 2: Deleting transactions without preserving an audit trail

Some software allows hard deletion; others encourage voiding or excluding. Prefer methods that preserve an audit trail and do not break bank feed integrity. If you must delete, ensure you still have evidence of the duplicate and why it was removed.

Trap 3: Piling on journal entries as a shortcut

Journal entries can be legitimate, especially for accounting adjustments, but using journals to “patch” missing invoices or duplicates can hide the underlying problem. If the error is transactional, fix the transaction. Use journals for genuine accounting adjustments that cannot be represented as a standard transaction.

Trap 4: Correcting only the summary totals

If your submission tool allows overriding totals, resist the temptation unless you are certain it is an accepted method and your digital records still support the figures. The strongest position is: “Our books show this, and our submission reflects our books.”

What to do if the error involves VAT elements

Some quarterly MTD submissions involve VAT reporting, either as part of VAT returns or as embedded tax elements within income and expenses. VAT errors are particularly important to correct because they affect the amount of tax collected or reclaimed.

If your mistake involves VAT:

• Confirm whether the error is a VAT rate issue (standard vs zero vs exempt), a recoverability issue (business vs private), or a timing issue (invoice date vs payment date schemes).

• Correct the VAT coding on the underlying transactions.

• Re-run the VAT report for the affected period and compare it to what was filed.

• If your VAT return for that quarter has already been filed, check whether your regime expects you to correct via a VAT adjustment in a later return or via an amendment process. Many VAT systems have specific rules about how to correct past-return errors.

The key is consistency: the VAT treatment in your transaction-level records should match the VAT figures you end up reporting.

When you should contact support or the tax authority

Many errors can be fixed internally by correcting your records and using an amendment or next-submission adjustment. However, certain cases justify escalating sooner rather than later:

Wrong entity submissions: Data sent to the wrong account or wrong taxpayer reference.

Duplicate submissions: You submitted the same quarter twice and both are showing as received, and your software cannot mark one as superseded.

Submission rejections or mismatches: The authority rejects your correction due to period rules, validation errors, or API issues that you cannot resolve.

Corrupted integration data: An app sync error mass-changed categories or duplicated hundreds of entries, and you need a rollback strategy.

Security concerns: You suspect unauthorised access or you see filings you did not make.

When contacting support, provide a concise summary: submission reference, period, what you attempted, screenshots of error messages, and the exact totals involved. This accelerates resolution and reduces back-and-forth.

Building a “quarterly close” checklist to prevent future mistakes

Correcting mistakes is useful, but preventing them saves time and stress. A simple quarterly close checklist can reduce the likelihood of errors:

1) Bank feed and import completeness

• Confirm all bank accounts are synced through the quarter end.

• Check for gaps in transaction dates.

• Confirm you have not imported the same file twice.

2) Reconciliation status

• Reconcile bank accounts to the quarter end.

• Investigate unreconciled items and duplicates.

3) Sales completeness

• Check invoice numbering continuity and missing invoice numbers.

• Compare sales totals to payment processor or POS summaries if relevant.

4) Expense completeness

• Confirm recurring bills are recorded (rent, utilities, subscriptions).

• Confirm large one-off purchases are supported by receipts.

5) Review categorisation and tax treatment

• Spot-check high-value items and unusual categories.

• Confirm private vs business treatment.

6) Draft submission review

• Generate the draft quarterly submission.

• Compare totals to internal management reports or last quarter trends.

• Investigate any large swings before submitting.

7) Submission archive

• Save confirmation receipt and exported report for the period.

• Add a short note on any assumptions or known minor timing differences.

Explaining corrections internally and to stakeholders

Even if the tax authority accepts corrections through the next submission, you may still need to explain what happened to someone else: a finance partner, an accountant, or your own management team. A simple explanation format helps:

What happened: “Quarterly update for Q2 understated income.”

Why: “Invoices from one sales channel were not imported due to an integration failure.”

Impact: “Income understated by £X; profit understated by £Y.”

Correction: “Imported missing invoices, reconciled receipts, and the next quarterly submission reflects corrected year-to-date totals.”

Prevention: “Added an import completeness check and monthly reconciliation before quarter end.”

This keeps the focus on control and remediation rather than blame.

Special considerations if you use an accountant or bookkeeper

If you work with a professional, coordinate corrections carefully. The most common coordination problems are duplicated effort and competing edits. Two people trying to fix the same ledger at the same time can create new inconsistencies.

Good practice includes:

• Agree who owns the correction: you or your accountant.

• Share the evidence package: what was submitted, what is wrong, and what you believe the correct figures are.

• Use the same cut-off date range when running reports so you are comparing like with like.

• Decide whether the fix is an amendment or will flow into the next quarter, and record that decision.

Even if you do your own bookkeeping, an accountant can be helpful when the error touches complex issues like VAT treatments, timing rules, or year-end adjustments.

What “good documentation” looks like for a corrected submission

You do not need a novel, but you do need enough to reconstruct the change later. A good correction file might contain:

• Original submission confirmation and totals.

• Corrected submission confirmation (if amended) or the next quarter submission that incorporates the correction.

• A before/after report for the quarter showing the key totals changing.

• A transaction-level list of what was added, removed, or recoded.

• Notes explaining why each change was made, including references to invoices or bank entries.

• A short prevention note describing what control you added.

This documentation is especially helpful if you are ever asked why totals moved between quarters or why a year-to-date number changed unexpectedly.

Putting it all together: a simple decision guide

If you want a quick way to decide what to do when you discover an error, use this guide:

If the submission is attached to the wrong entity or taxpayer reference: capture evidence and contact support/authority; then submit correctly under the right account.

If the quarter date range is wrong or overlaps: correct the reporting period and amend/resubmit if your system supports it; ensure later quarters are refreshed.

If transactions are missing, duplicated, or miscategorised: correct the underlying records first; then either amend the quarter (if needed) or allow the correction to flow into the next submission (if your regime supports cumulative updates).

If the issue is caused by mapping/integration: fix the mapping first, then fix the data, then correct the submission route; otherwise the problem will recur.

If the mistake relates to year-end adjustments: correct the records and ensure the finalisation step captures the correct position, while still keeping quarterly data as accurate as reasonably possible.

Conclusion: corrections are normal, but the method matters

Mistakes in quarterly MTD submissions happen for straightforward reasons: missing data, duplicates, period confusion, integration quirks, or simple human error. The goal is not to panic or to try to “hide” the mistake, but to correct it in a way that keeps your digital records consistent with what you report.

The most reliable approach is to start with a clear identification of the issue, preserve evidence of what was submitted, correct the underlying transaction records, and then choose an appropriate route—amend if necessary, allow corrections to flow through the next update when suitable, or finalise at year-end for adjustments that genuinely belong there. Along the way, document what changed and why, and put a small preventive control in place so the same error does not return next quarter.

When you follow that disciplined process, correcting quarterly MTD mistakes becomes routine rather than stressful. Your books remain trustworthy, your submissions become easier to prepare, and you spend less time firefighting and more time running your business.