VAT returns & submissions

Your VAT keeps getting flagged — signs your current practitioner is the problem

VAT returns flagged repeatedly? Learn the warning signs that your practitioner is underperforming and how to spot them before costs pile up.

Your SARS correspondence keeps landing in your inbox with "query" or "adjustment" stamped on it. Your VAT refunds are taking longer than they should. You're not sure if your practitioner made a mistake or if SARS is just being thorough, and you're left sitting in uncertainty, possibly owing money you didn't think you owed. At this point, most business owners wonder: is this normal friction, or is my practitioner the weak link?

The answer often becomes clear once you know what to look for. Bad VAT practice leaves a trail — and catching it early saves you stress, penalties, and cash.

When flags and queries point to sloppy input records

SARS doesn't flag returns randomly. If you're getting repeated queries on the same line items — input VAT claimed, exempt supplies, or zero-rated goods — the problem is usually upstream. Your practitioner may be accepting what you hand over without questioning it, or worse, not asking you the right questions in the first place.

A practitioner who doesn't drill into *why* you're claiming input VAT on a particular invoice, or who doesn't cross-check your supplier invoices against your purchase ledger, is doing surface-level work. They should spot mismatches between what you've recorded and what's actually invoiced. If SARS is catching errors that your practitioner missed, you're paying twice: once in time managing the query, and again in interest or penalties.

Ask yourself: does your practitioner ask you to justify specific claims, or do they just take your figures and file them? The first approach is slower upfront but bulletproof. The second is cheap and brittle.

Missing deadlines and late submissions are a red flag

VAT returns have hard filing dates. There's no grace period, no "close enough." If your practitioner is regularly submitting late — even by a few days — SARS assesses penalties automatically. Some practitioners blame clients for slow record-keeping, and sometimes that's fair. But a practitioner worth hiring should flag the deadline months ahead, set a clear cut-off date for your documents, and manage the workflow so you're never scrambling at the last moment.

Late submissions also trigger SARS's automated compliance algorithms. Once you're flagged as a chronic late filer, SARS scrutinises your returns more heavily. Your subsequent submissions get picked apart, even if they're correct, simply because your filing history looks unreliable. A good practitioner protects you from this cycle by building in buffer time and holding you to it.

If you're constantly chasing your practitioner for confirmation that your return has been filed, or if you find out about a missed deadline through a SARS letter, that's a sign they don't have the systems or discipline for VAT work.

Vague explanations and poor communication when things go wrong

When a query arrives, a competent practitioner explains it clearly: here's what SARS is asking, here's why they're asking it, and here's how we'll respond. They show you the evidence, walk you through the logic, and keep you in the loop.

Instead, some practitioners go quiet, or they send a one-liner saying "SARS wants more info on this input" without explaining what went wrong or how to prevent it next time. That's a sign they don't fully understand the return themselves — they're just reacting to SARS rather than staying ahead of compliance.

Common warning signs include:

Your practitioner doesn't send you copies of submitted returns to review before filing
They can't explain why a particular treatment was chosen
They blame you or SARS whenever something goes wrong, without offering solutions
They take weeks to respond to your queries about a SARS letter

The cost of finding out too late

Many business owners only switch practitioners after they've been stung. But by then, they're already dealing with back-taxes, interest, and possibly penalties. Some run into cash flow problems because they suddenly owe a large adjustment they didn't budget for.

A practitioner who communicates clearly, asks tough questions, meets deadlines, and explains their reasoning protects you long before a crisis arrives. If you're getting flagged repeatedly, or if your gut is telling you something's off, trust that signal. You don't need to wait for a catastrophe to make a change.

When you're ready to find someone better, look for a practitioner who asks to see your full invoice files, who discusses treatment decisions with you upfront, and who has a clear system for meeting deadlines. Strove lets you find verified local bookkeeping and accounting professionals, read their experience, and check their credentials — so you can make a switch with confidence, knowing you're handing your VAT to someone with a track record.

Common questions

How often should I expect SARS to query my VAT return?: Occasional queries are normal, especially if you claim significant input VAT or operate across multiple categories of supply. But repeated queries on the same issues, or queries every period, suggest your practitioner isn't catching errors before submission. A well-run return should be queried rarely, and when it is, usually for one-off issues rather than systemic problems.
Can I hold my practitioner liable if their mistakes cost me penalties?: That depends on your service agreement and the nature of the error. Some practitioners carry professional indemnity insurance; others don't. Before switching, ask any new practitioner whether they're insured and what their complaints process is. Check also that your current agreement spells out who's responsible if something goes wrong.
What should I do if I'm mid-year and want to switch practitioners?: You'll need to authorise SARS to release your records to the new practitioner and ensure a clean handover of all your documents and filing history. Don't leave a gap — the new practitioner should take over before the next return is due. A professional switch is straightforward if both practitioners co-operate.
Does a cheap VAT practitioner always mean poor work?: Not always, but low fees often reflect less attention to detail, fewer support hours, and lighter documentation. Compare what you're getting for the price — do they offer monthly bookkeeping support, regular compliance reviews, or just the filed return? Practitioner quality and cost don't always align, so judge by their process and communication, not just price alone.

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More on VAT returns & submissions

When flags and queries point to sloppy input records

Missing deadlines and late submissions are a red flag

Vague explanations and poor communication when things go wrong

Common warning signs include:

Your practitioner doesn't send you copies of submitted returns to review before filing

They can't explain why a particular treatment was chosen

They blame you or SARS whenever something goes wrong, without offering solutions

They take weeks to respond to your queries about a SARS letter

The cost of finding out too late

Common questions

How often should I expect SARS to query my VAT return?

Occasional queries are normal, especially if you claim significant input VAT or operate across multiple categories of supply. But repeated queries on the same issues, or queries every period, suggest your practitioner isn't catching errors before submission. A well-run return should be queried rarely, and when it is, usually for one-off issues rather than systemic problems.

Can I hold my practitioner liable if their mistakes cost me penalties?

That depends on your service agreement and the nature of the error. Some practitioners carry professional indemnity insurance; others don't. Before switching, ask any new practitioner whether they're insured and what their complaints process is. Check also that your current agreement spells out who's responsible if something goes wrong.

What should I do if I'm mid-year and want to switch practitioners?

You'll need to authorise SARS to release your records to the new practitioner and ensure a clean handover of all your documents and filing history. Don't leave a gap — the new practitioner should take over before the next return is due. A professional switch is straightforward if both practitioners co-operate.

Does a cheap VAT practitioner always mean poor work?

Not always, but low fees often reflect less attention to detail, fewer support hours, and lighter documentation. Compare what you're getting for the price — do they offer monthly bookkeeping support, regular compliance reviews, or just the filed return? Practitioner quality and cost don't always align, so judge by their process and communication, not just price alone.