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Seven Costly VAT Mistakes Small Businesses Make and How BES Accountancy Fixes Them Before HMRC Notices

Writer: bes Accountancy Services
bes Accountancy Services
Oct 15
4 min read

VAT mistakes small businesses make often begin with everyday record keeping problems. Incorrect VAT coding, missing invoices, duplicated purchases, weak digital records and transactions entered in the wrong period can all lead to inaccurate returns. For businesses in London, the best defence is to keep records current, reconcile them before filing and correct errors through the proper HMRC process.


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Seven VAT Mistakes Small Businesses Make


Using The Wrong VAT Treatment


Not every sale or purchase has the same VAT treatment. Businesses can make errors by applying the wrong rate, treating an exempt supply as taxable, or assuming that VAT on every cost can be reclaimed. Once the coding is wrong, the return can also be wrong. BES Accountancy can review transaction coding, source documents and VAT settings before submission.


Reclaiming VAT Without Adequate Evidence


Input VAT claims generally need appropriate documentary evidence. A bank payment alone does not automatically establish that VAT can be reclaimed. Missing or incorrect supplier invoices can therefore create problems. Good bookkeeping means matching purchase entries to suitable evidence and resolving gaps before filing.


Missing Sales Or Recording Purchases Twice


A missing sales invoice can understate output VAT. A duplicated purchase invoice can overstate recoverable VAT. These mistakes are more likely when bookkeeping is updated in batches or data comes from several sources. Regular reconciliation between sales, purchases, bank activity and the VAT account is an effective control before a return is finalised.


Weak Making Tax Digital Records


HMRC requires specified VAT records to be kept digitally under Making Tax Digital unless an exemption applies. Where more than one software product is used, required transfers of VAT data must use digital links rather than manual copying and pasting. BES Accountancy has expertise in Xero and QuickBooks and can support cleaner digital bookkeeping and consistent VAT coding. HMRC’s guidance on keeping VAT records explains the current requirements.



Putting Transactions In The Wrong VAT Period


VAT reporting is not always determined by the date money reaches the bank. The correct period can depend on time of supply rules and, where relevant, the accounting scheme in use. Posting a transaction to the wrong period can shift VAT between returns and create reconciliation differences later.


Filing Or Paying Late


HMRC operates a points based system for late VAT Returns. Once the relevant threshold is reached, a £200 penalty applies, with further £200 penalties for subsequent late submissions while the business remains at the threshold. Late payment penalties can also apply when VAT remains unpaid more than 15 days after the due date.


Finding An Error And Doing Nothing


A discovered VAT error should not simply be carried forward. HMRC allows certain errors from earlier returns to be corrected on a later VAT Return, subject to limits. Net errors of £10,000 or less can generally be adjusted on the next return. Errors between £10,000 and £50,000 can also qualify if they are less than 1 per cent of total sales. Errors outside those limits, and deliberate errors, must be notified separately.



How Better VAT Bookkeeping Protects Cash Flow


VAT is not just a filing exercise. If the VAT account is inaccurate, a business can misunderstand how much cash is genuinely available, overlook recoverable VAT or face an unexpected liability close to the payment date.


Accurate bookkeeping, regular reconciliations and well configured digital accounting give owners better visibility before a return is filed. They also make financial information easier to prepare for accountants, lenders and other professional advisers.


Besnik Vata, Director of BES Accountancy, explains:


“Accurate VAT reporting starts with complete records, consistent coding and regular reconciliation. Problems are easier to correct when they are identified early.”

BES Accountancy is a London based accounting company founded in 2020 and supports businesses and self employed professionals across the UK with VAT, bookkeeping and computerised accounting.




Final Thoughts


The most costly VAT mistakes small businesses make often begin with ordinary bookkeeping issues, such as a missing invoice, an incorrect VAT code or a duplicated transaction. The solution is to maintain reliable records throughout the period and investigate exceptions before submission.


For London businesses and clients across the UK, BES Accountancy can support VAT reporting, bookkeeping, Xero and QuickBooks processes with a practical focus on availability, efficiency and trust. Circumstances differ, so businesses with uncertain VAT treatment or historic errors should seek advice based on their specific position.








Frequently Asked Questions


What Are The Most Common VAT Mistakes Small Businesses Make?


Common problems include incorrect VAT treatment, unsupported input VAT claims, missing sales, duplicated purchases, weak digital records, transactions posted to the wrong period and errors that are left uncorrected.



Do VAT Registered Businesses Have To Keep Digital Records?


Most VAT registered businesses within Making Tax Digital must keep specified VAT records digitally unless an exemption applies. The software and records used should meet HMRC requirements.



How Long Should A Business Keep VAT Records?


HMRC generally requires VAT records to be kept for at least six years, although different rules can apply in particular schemes or circumstances.



Can A VAT Return Error Be Corrected After Submission?


Yes. HMRC provides methods for correcting VAT Return errors, but the correct route depends on the amount and nature of the error. Some errors can be adjusted on a later return, while others must be notified separately.



Internal resources to explore next

  • Learn about our team and values on the About us page.

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  • Keep learning with more insights on the BES blog.

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