Important: This guide describes general record-keeping practice as at 17 July 2026. It is not individual accounting, tax, or legal advice. Ask a Czech adviser about a disputed payment, set-off, credit note, foreign currency, or material balance.
You issue a Czech invoice for CZK 24,200.00, but the client sends CZK 12,100.00. A corporate customer settles three invoices in one transfer. An international bank deducts a fee before the money reaches you. Or a customer pays twice. Each event creates a bank entry, but none should be treated as a fully settled invoice until you can explain the amount.
This matters especially to a foreign OSVČ (osoba samostatně výdělečně činná, a Czech sole trader) who receives payments from several countries or payment providers. Reliable reconciliation keeps three records separate: the invoice, the bank movement, and the remaining receivable. The Czech variabilní symbol (variable symbol or VS) helps identify a payment; it does not prove that the amount is complete.
A safe reconciliation sequence
- Identify the bank entry. Check the receiving account, payer, VS, message, amount, currency, value date, and any bank reference.
- Establish the customer’s intention. Decide which invoice or invoices the transfer covers. Obtain a remittance advice or email if the reference is unclear.
- Allocate exact amounts. Keep each invoice’s original total and subtract only payments supported by the evidence.
- Record exceptions separately. An overpayment, refund, or bank charge is not another name for the invoiced price.
- Close an invoice only at zero balance. “Paid” should mean no amount remains outstanding, not merely that some money arrived.
Invoice-to-bank decision table
| Invoice | Bank movement | Remaining balance | Action |
|---|---|---|---|
| CZK 10,000.00; VS and currency match | +CZK 10,000.00 | CZK 0.00 | Match it and, after checking for duplicates, mark the invoice paid |
| CZK 24,200.00 | +CZK 12,100.00 | CZK 12,100.00 | Record a part payment, keep the invoice open, and request the balance |
| CZK 10,000.00 | +CZK 10,500.00 | CZK 0.00 plus CZK 500.00 overpayment | Agree a refund or another documented use of CZK 500.00 |
| I1 CZK 8,000.00 + I2 CZK 4,000.00 | +CZK 12,000.00 in one transfer | CZK 0.00 on each after allocation | Split the movement 8,000.00/4,000.00 and retain the client’s breakdown |
| CZK 20,000.00 | +CZK 19,750.00 after a CZK 250.00 fee | CZK 250.00 unless agreed otherwise | Separate the gross settlement from the fee; do not silently discount the invoice |
| CZK 15,000.00; wrong VS | +CZK 15,000.00 | CZK 0.00 only after identification | Verify the payer and purpose, then match manually with a note |
1. Exact payment
The clean case is an invoice for CZK 10,000.00 followed by one CZK 10,000.00 credit with the correct VS. Still check that the same customer does not have another invoice for the same amount and that the movement has not already been used. Once identified, allocate the full amount and reduce the receivable to zero.
This is the supported automatic path in Taxorio. The current Taxorio payment-matching help says that an unambiguous match of the variable symbol and exact CZK amount can mark the invoice paid automatically. The repository matcher also prevents automatic confirmation where the best candidate is ambiguous, the payment is not a reliable full-amount CZK match, or the invoice is a pro forma. Less certain suggestions require human review in the Bank section.
2. Partial payment
Suppose the customer pays CZK 12,100.00 against a CZK 24,200.00 invoice. The receipt is real, but the invoice still has a CZK 12,100.00 receivable. Record the instalment date and amount in a traceable subsidiary record, tell the customer what remains, and keep the original invoice intact.
The current Taxorio implementation does not prove an automatic instalment ledger that accumulates several part payments against one running balance. A lower transfer must not automatically become “paid in full.” Keep the invoice open in Taxorio and handle the partial balance and final status manually after the whole amount has been reconciled. If your workflow needs detailed instalment accounting, agree the system of record with your accountant.
3. Overpayment or duplicate transfer
A client transfers CZK 10,500.00 for a CZK 10,000.00 invoice. The invoice principal is covered, but the extra CZK 500.00 is not automatically additional revenue for that supply. Contact the client. Return it, or apply it elsewhere only under a clear agreement and with supporting documents. A duplicate payment follows the same logic: an invoice cannot be paid twice merely because the bank has two credits.
When refunding, use a bank message that identifies the original receipt and retain both entries. Do not amend the original invoice price to force it to agree with the net cash. If the commercial price itself changes because of a discount, cancellation, or complaint, Czech VAT and invoicing rules may require a corrective tax document; that is a different event from returning money sent by mistake.
4. One transfer for several invoices
A customer pays CZK 12,000.00 to settle invoice I1 for CZK 8,000.00 and I2 for CZK 4,000.00. Ask for a remittance advice listing both invoice numbers and amounts. Create two logical allocations whose sum equals the single bank movement. Each invoice then reaches zero without inventing a second bank transaction.
Taxorio’s current implementation does not establish automatic one-to-many splitting. Do not accept the first suggested invoice merely because its VS appears in the message. Document the allocation outside the automatic match and update each invoice only after checking the total. If the payment is insufficient, obtain the customer’s allocation or agree which receivable is paid first, then preserve the balance on the other invoice.
5. A bank fee deducted before receipt
This is common with cross-border transfers. Your invoice is CZK 20,000.00; the customer’s confirmation shows CZK 20,000.00 sent; only CZK 19,750.00 reaches your account because CZK 250.00 was deducted. Check the contract, the payment instruction (including any fee-sharing choice), and bank evidence. Unless the shortfall is yours under the agreement, the invoice still has CZK 250.00 outstanding.
Do not reduce the invoiced consideration after the event merely to match the net credit. Where you agreed to bear the charge, the fee will normally need separate supporting evidence and separate treatment as a bank expense, while the gross settlement remains explainable. The exact entry depends on whether you keep Czech daňová evidence (tax records) or statutory accounts and on what the bank document shows.
6. Wrong or missing variable symbol
An exact amount without the right VS is a clue, not conclusive evidence. Compare the payer’s name and account, bank message, date, open receivables, and the client’s confirmation. Only then make a manual allocation and record why it was reasonable.
Taxorio normalises a numeric VS padded by a bank with leading zeroes, so “0020260009” can correspond to “20260009.” It does not invent a different or absent identifier. An amount-only resemblance, especially where several invoices share the amount, should remain for review rather than automatic closure.
7. Refund to the customer
A refund is a separate outgoing bank movement. Link it to the incoming payment and its reason. For a CZK 500.00 overpayment, a complete trail might contain the CZK 10,000.00 invoice, a CZK 10,500.00 receipt, the customer’s email, and a CZK 500.00 outgoing refund. The net amount retained against the invoice is then CZK 10,000.00.
If you refund part of the agreed price because the supply is reduced, defective, or cancelled, a bank transfer alone does not correct the underlying tax document. A Czech VAT payer may need to apply the correction rules in Act No. 235/2004 Coll., the Czech VAT Act. Distinguish a return of money that was never due from a commercial reduction of the invoiced supply.
8. Outstanding balance at year end
At 31 December, reconcile every open invoice to actual bank movements. If a CZK 24,200.00 invoice has only a CZK 12,100.00 December payment, the year-end receivable is CZK 12,100.00. A January bank statement can confirm what happened next, but a customer’s promise or transfer instruction is not the same as received cash.
An OSVČ using tax records under Section 7b of the Czech Income Tax Act must establish the actual state of receivables and liabilities at year end. Cash income is normally recorded when received; Czech statutory accounting and VAT follow different timing rules. See the companion guide on when a Czech sole trader taxes an invoice and the Czech Financial Administration’s official OSVČ income-tax information.
Before you mark a Czech invoice paid
- The sum of evidenced allocations equals the full invoice amount.
- Every bank movement is used once, and any split is reproducible.
- Overpayments, refunds, and bank charges are separate from the invoice price.
- The payment date comes from bank evidence, not the issue date or due date.
- Any unpaid amount remains visible as a receivable at year end.
Automation is valuable for a clean one-payment-to-one-invoice match. When money is short, excessive, combined, or returned, the priority changes: preserve an audit trail. That trail lets you show what was received, which receivable it settled, what remains open, and why the invoice status was changed.