The mental maths most business owners do is simple: take sales, take 20%, that's roughly the VAT bill. The actual figure on the return often comes in higher, and the gap isn't usually an error; it's one or more of a handful of things that a rough percentage-of-sales estimate can't see.
Input VAT you can't actually reclaim
Not every VAT charge on a purchase is reclaimable, even for a fully taxable business. The most commonly blocked categories:
- Business entertainment: VAT on client entertainment (meals, hospitality, event tickets for clients) is blocked entirely. Staff entertainment, within reasonable limits, is usually fine, the two get mixed up on expense claims more often than you'd think.
- Most cars: Input VAT on car purchases is almost never reclaimable unless the vehicle is used 100% for business with genuinely no private use available, a very high bar. Vans and other commercial vehicles are a different story and are usually fully reclaimable.
- Non-business use: Any element of a purchase used privately rather than for the business has its VAT blocked, or apportioned if the use is mixed.
A business that assumes every purchase invoice carries reclaimable VAT will consistently under-forecast its net VAT bill.
Partial exemption
If your business makes both taxable and VAT-exempt supplies (common in areas like some financial services, insurance, education, and health-related work), input VAT that relates directly to the exempt side can't be reclaimed at all, and VAT on general overheads has to be apportioned between the two. There's a de minimis limit that lets you ignore small amounts of exempt-related input VAT, but once you're over it, the disallowed portion can be a meaningful, easy-to-miss addition to the bill.
| Sales (VAT-exclusive) | £80,000 |
| Naive estimate: 20% of sales | £16,000 |
| Output VAT at 20% | £16,000 |
| Less: input VAT reclaimed on purchases | −£2,100 |
| Add: reverse charge output VAT self-accounted | +£1,400 |
| Actual VAT due | £15,300 |
In that example the naive estimate happens to land close to the real figure, but only by coincidence: the input VAT reclaim and the reverse charge addition move in opposite directions and roughly cancel out. Change either one and the estimate stops being useful, which is exactly why a single "20% of sales" rule of thumb is unreliable even when it looks right.
Reverse charge supplies add VAT you didn't collect from anyone
If you buy in services subject to the domestic reverse charge (construction services under CIS, or services from overseas suppliers), you self-account for output VAT on that purchase in box 1 of your own return, and typically reclaim the same amount as input VAT in box 4. If your business isn't fully VAT recoverable, or the reverse charge supply falls in a different quarter than expected, this can move the net figure in ways that look confusing without knowing the mechanism.
Flat rate scheme's gross-turnover quirk
If you're on the flat rate scheme, your VAT bill is a percentage of gross, VAT-inclusive turnover, not net sales. A business assuming its flat rate percentage applies to net sales will consistently underestimate what's actually due: the base the percentage is applied to is bigger than they think. Combined with the limited cost trader rule pushing many service businesses to 16.5%, flat rate VAT frequently comes in higher than a standard-scheme business would expect to pay on the same turnover.
⚠️ Errors on a previous return can also show up here. If a net error on an earlier return was over £10,000 (or a smaller threshold tied to turnover), it has to be reported to HMRC separately rather than simply adjusted on the current return, and can trigger an additional payment. Smaller errors can usually just be corrected on the next return, but the correction still changes what's due that quarter.
Don't forget the relief you might be owed
The gap isn't always in HMRC's favour. If you've written off unpaid customer invoices as bad debts, you may be entitled to bad debt relief, reclaiming the output VAT you already accounted for on an invoice that's now over six months old and formally written off. It's easy to miss because it requires an active claim rather than happening automatically under standard VAT rules.
💡 Rooby tip: Rooby shows the full VAT breakdown for eligible clients (output VAT, input VAT, the number of sales and purchase invoices and credit notes involved, and the bank transactions checked against them) rather than a single top-line number, so it's clear exactly where the figure comes from.
Checking a bill that looks wrong
- Get the box-by-box breakdown from your accountant or bookkeeping software, not just the net figure
- Check which VAT scheme is actually being used, standard, cash accounting, or flat rate
- Confirm whether any reverse charge supplies were involved in the period
- Check for blocked input VAT categories (entertainment, cars, non-business use)
- Review whether a prior period error or adjustment has fed into the current return
Almost every "the VAT bill is higher than I expected" conversation traces back to one of these. Finding which one applies to your business also tells you whether there's a genuine planning opportunity: reclaiming bad debt relief, reviewing scheme choice, or simply building a better forecast next time.
Rooby calculates VAT from your actual Xero data (invoices, credit notes, and bank transactions), with the full workings shown, not a rough percentage.