The short answer, explained
Most inspections are pre-arranged. HMRC writes proposing a date and lists what it wants to see, giving you time to prepare rather than turning up unexpectedly.
On the day, or through correspondence if it's a desk-based check, an officer works through your VAT returns comparing them to underlying invoices, your accounting system, and how supplies have been treated for VAT purposes.
The officer will typically ask questions about how the business works: what you sell, who your customers are, how you price and invoice. This context helps them judge whether the VAT treatment makes sense, not just whether individual figures tie up.

