How Do You Invoice Clients When Payment Is Split Across Multiple Methods?

Why split-payment invoicing needs a clear plan

Split payments are becoming normal. A client might cover part of an invoice by bank transfer, pay a deposit by card, and settle the remainder via PayPal or cash. Sometimes the split happens because of internal approval limits, currency preferences, project milestones, or because different departments are paying different portions. Whatever the reason, the invoicing question is the same: how do you issue one invoice that stays accurate, easy to audit, and simple for your client to pay?

The good news is that split-payment invoicing is not complicated when you structure your invoice and your recordkeeping properly. You need an invoice layout that makes totals unambiguous, a method of documenting each payment method used, and a system that keeps the balance due correct in real time. This is exactly the kind of workflow invoice24 is built to handle: one professional invoice, multiple payment methods, clear payment history, and a balance that always matches what’s actually owed.

In this guide, you’ll learn practical ways to invoice clients when payment is split across multiple methods, the mistakes to avoid, and how to keep your books and your client’s experience clean from start to finish.

Start with the simplest principle: one invoice, one source of truth

A common mistake is to create multiple invoices to match payment methods. For example, a freelancer might issue one invoice for the card payment and another for the bank transfer. That sounds tidy, but it usually creates bigger problems: duplicate revenue entries, confusion about what the total work cost was, and a higher chance of under- or over-collecting. It also makes client approvals harder because procurement teams typically want one invoice number for one set of deliverables.

The best approach in most cases is to issue one invoice that represents the full amount due for the work delivered. Then you record multiple payments against that single invoice, each with its own method, date, reference, and amount.

invoice24 makes this approach straightforward: you create one invoice and then apply as many payments as needed. Each payment entry can include a payment method label (bank transfer, card, PayPal, cash, cheque, etc.) and a note such as a transaction reference or bank remittance ID. That way, your invoice remains your source of truth, and your payment history becomes a clear timeline rather than a maze.

Decide whether you’re dealing with a “split payment” or a “partial payment”

Before you format anything, clarify what type of split you’re handling. These terms get mixed up, but the distinction matters for communication and reporting.

Split payment usually means the client intends to pay the total invoice amount using two or more methods, often within the same payment window. For example: £1,000 by bank transfer and £200 by card.

Partial payment often implies the invoice will be paid over time (instalments), and the payment method might be the same or change from payment to payment. For example: £500 now, £500 next month, £200 later.

In practice, you may have both: an instalment plan where each instalment is paid via different methods. The invoicing structure can be identical (one invoice, multiple payments), but the message to the client is different. If it’s instalments, you should include the schedule or milestones more clearly.

In invoice24, you can handle both situations cleanly by recording each payment as it arrives. The invoice balance updates automatically, so the client can always see what is still outstanding.

How to structure the invoice so split payments are obvious

A split-payment-friendly invoice has three jobs: show the total, show what’s been paid so far, and show what’s still due. The last two pieces can appear as a “Payments received” section or as a running balance, depending on your style and what your clients prefer.

Here’s a practical structure you can use:

1) Standard invoice header: invoice number, issue date, due date, your business details, client details, and any PO number.

2) Line items: products/services, quantities, rates, discounts, tax/VAT where applicable.

3) Totals: subtotal, tax, total invoice amount.

4) Payments received (optional on first issue, essential after payments begin): list each payment with date, method, amount, and reference.

5) Balance due: total minus payments received.

6) Payment instructions: show multiple ways to pay (bank transfer details, card link, PayPal email, etc.) and indicate what reference to include.

invoice24 supports all of this in a clean, professional template. You can present multiple payment options without clutter, and once payments start arriving, you can keep the invoice record accurate without rewriting the invoice each time.

Should you mention the split on the first invoice?

Sometimes you know in advance that the client will split the payment. Other times you only find out when the first payment arrives and it’s not the full amount. If you know ahead of time, mentioning it can reduce confusion for both sides.

On the initial invoice, you can include a short note in the “Notes” or “Payment terms” area, such as:

“Client will pay £X by bank transfer and £Y by card. Please include invoice number as payment reference.”

This is especially useful for larger invoices where the client is coordinating payment across departments or where card payments have caps. It can also help your own team reconcile quickly.

With invoice24, you can add clear notes and keep your payment instructions consistent. That way the client has one place to look for what they’re doing and why.

How to record multiple payment methods correctly

Recording split payments correctly means capturing enough detail to reconcile later without turning your invoice into a novel. A simple rule is: record what you’d want to see if someone asked you, six months from now, to prove how the invoice was paid.

For each payment, capture:

Date received: the day the funds cleared or you received confirmation.

Amount: exactly what was received.

Method: bank transfer, card, PayPal, cash, cheque, direct debit, etc.

Reference: bank transaction reference, payment processor transaction ID, cheque number, or “cash receipt #”.

Notes (optional): payer name if different, department, or any context like “Deposit for phase 1”.

invoice24 is designed for this. You can log payments against the invoice with a method label and reference, so your payment trail remains clear. And because the balance updates instantly, you avoid the classic issue of emailing clients asking for money they already sent via a different channel.

One invoice vs multiple invoices: when multiple invoices might actually make sense

While “one invoice, multiple payments” is the best default, there are a few legitimate cases where issuing separate invoices is reasonable:

Separate legal entities paying: If two different companies are paying different parts, they may require separate invoices issued to each entity for their own accounting.

Separate tax treatments: If part of the work is taxable and part is not, or if different jurisdictions apply, you may need separate invoices for compliance.

Separate deliverables and approvals: If procurement requires separate invoices tied to separate purchase orders, splitting invoices might be necessary.

Even then, be cautious. If you split invoices, ensure each invoice clearly describes the deliverables it covers so the combined amount still matches what was agreed. In invoice24, you can create separate invoices quickly and keep the numbering, client records, and payment tracking consistent so you don’t lose the thread.

Handling deposits paid by one method and the remainder by another

A very common split scenario is a deposit (often paid by card for speed) and a remainder (often paid by bank transfer). The best way to handle this depends on how you prefer to document deposits.

Option A: Invoice the full amount and record the deposit as a partial payment

This is clean when the client agrees to the full scope and price upfront. You issue one invoice for the full amount. When the deposit arrives, you record it as a payment. The balance due remains visible.

Option B: Issue a deposit invoice, then a final invoice

This is useful when the deposit is tied to scheduling, onboarding, or a pre-production phase and you prefer not to invoice the entire amount until later. You issue a deposit invoice first. Once you deliver or reach the next milestone, you issue a final invoice (either for the remaining amount or for the full amount with the deposit credited, depending on your local norms).

invoice24 can support either approach. If you want maximum simplicity for the client, Option A keeps everything on one invoice. If you want milestone clarity, Option B can be more explicit. The key is consistency and making sure your client always knows what the deposit is for and what remains outstanding.

Including multiple payment options without confusing your client

Offering many payment methods is great for getting paid faster, but it can overwhelm clients if the instructions are messy. The solution is to keep your payment section structured and to give clients a simple rule: choose one method or split across methods, but always include the invoice number as the reference.

A tidy payment instruction block might include:

Bank transfer: account name, IBAN/sort code, account number, and the reference they must include.

Card payment: a secure payment link or “Pay now” button if your workflow supports it.

PayPal: PayPal email or link, plus reference instructions.

Cash/cheque: where to deliver and how you will issue a receipt.

invoice24 helps you present these options clearly so the invoice still looks professional. The goal is to reduce friction: the easier it is to pay, the sooner the money arrives.

What to do when the client pays using unexpected methods

Sometimes a client surprises you. You requested bank transfer, but they send half via card and half via PayPal. Or they pay via two bank transfers from different accounts. The invoicing response should be calm and systematic:

1) Record what actually happened: log each payment against the invoice with the method and reference.

2) Update the client with the current balance: a short email confirming receipt and what’s left (if anything) prevents misunderstandings.

3) If fees are involved, decide how you handle them: some businesses absorb card or PayPal fees; others pass them on. Whatever you do, keep it consistent and transparent.

In invoice24, once you record the payments, the invoice balance tells you what to do next. If the invoice is fully paid, you can mark it accordingly and send a receipt if needed.

How to show fees when different payment methods charge different costs

Payment processors often charge fees, and different methods have different costs. If you pass on fees to clients (where permitted), be clear about it before they pay, and show the fee as its own line item so totals remain understandable.

For example, you might include a line item such as “Card processing fee” or “PayPal transaction fee” if the client chooses that method and you’ve agreed the fee is payable. Alternatively, you can add a discount for bank transfer if you prefer a more positive framing.

The important thing is that fees should not appear as mysterious shortfalls. If you invoice £1,000 and you receive £970 because fees were deducted, it looks like the client underpaid unless you document what happened. The clean approach is for the client to pay the invoice amount in full and treat fees separately according to your policy and local rules.

invoice24 makes it easy to add clear line items and keep your invoice totals correct, whether you’re including fees, discounts, or method-specific adjustments.

Best practice: send receipts or payment confirmations for each payment

When a client pays an invoice in parts, they often need internal confirmation for each payment. A procurement team might need proof that the card deposit cleared before they approve the bank transfer. Or the client’s finance team may be matching your invoice to multiple remittance advices.

It helps to provide a short confirmation each time you receive a payment, including:

“Payment received: £X via [method] on [date]. Remaining balance: £Y. Invoice: [number].”

Some businesses do this manually via email, but the most reliable approach is to keep your invoice system updated so you can quickly generate a current statement of what’s paid and what’s due. invoice24’s payment tracking is perfect for this: the invoice remains accurate, and you can always share the latest balance without doing mental arithmetic.

How to handle split payments across currencies

Occasionally, clients split payments across currencies. For example, a client might pay part in USD via card and part in GBP via bank transfer. This introduces exchange rates, conversion fees, and timing differences.

To keep this manageable:

Choose an invoice currency: the invoice should have one primary currency for the total and balance due.

Document the agreed conversion approach: specify whether you’ll use the bank’s rate, the card processor’s rate, or a specific published rate at a certain time.

Record what you actually received: if you receive a converted amount, note it in payment notes and reconcile any difference as an exchange gain/loss according to your accounting practices.

If you regularly invoice internationally, having an organised system is essential. invoice24 keeps your invoice totals stable and your payment history detailed, which is exactly what you need when exchange rates add complexity.

Split payments across multiple stakeholders or departments

In B2B situations, it’s common for different departments to cover different portions. Marketing might pay for creative, IT might pay for integration, and finance might cover project management. They may still want one invoice, but they might ask you to break down the costs in a way that matches their internal budgets.

You can make this easier by:

Grouping line items by category: “Design,” “Development,” “Consulting,” “Licences,” etc.

Using clear descriptions: tie each group to a department or cost centre if requested.

Adding a note about who is paying what: “Marketing team paying £X; IT team paying £Y,” if the client wants that documented.

invoice24 lets you create clean line item groupings and keep notes on the invoice, so your client can route payments internally without asking you for multiple revisions.

What to do if a split payment creates a small underpayment or overpayment

Split payments can lead to tiny mismatches: a client rounds down a transfer, or a conversion results in a small difference, or a fee gets deducted unexpectedly. Handle these situations with a consistent policy:

Underpayments: If it’s a meaningful amount, request the remainder politely and promptly. If it’s a trivial amount, decide whether you write it off or carry it to the next invoice, but be consistent.

Overpayments: Confirm with the client whether they want a refund or a credit toward future work. Keep records clear so the overpayment doesn’t sit as a mystery in your accounts.

In invoice24, you can see exactly what’s been paid versus what was invoiced. That visibility makes it much easier to spot a £2.17 mismatch before it becomes a months-long confusion.

How to avoid reconciliation headaches

Reconciliation problems usually come from missing references, inconsistent invoice numbers, or payments not being recorded against the correct invoice. Split payments amplify those risks. The fix is process discipline:

Always require the invoice number as the payment reference: say it clearly in your payment instructions.

Record each payment immediately: don’t wait until month-end.

Keep payment notes consistent: if you track bank references, track them every time.

Don’t change the invoice total after payments begin: if something changes, issue an adjustment or a new invoice rather than editing history.

invoice24 helps because it centralises invoice and payment history. Instead of relying on spreadsheets, inbox searches, and payment processor dashboards, you keep everything connected to the invoice record where it belongs.

Communicating split-payment terms without sounding difficult

Clients appreciate clarity more than flexibility. You can be easy to work with and still be specific. Here are friendly ways to set expectations:

For split methods: “You’re welcome to split payment across bank transfer and card. Please include the invoice number as reference for each payment so we can match it quickly.”

For deposits: “A deposit of £X is due to confirm the booking. The remaining balance of £Y is due by [date].”

For multiple transfers: “If you need to pay in two transfers, no problem—just use the same invoice number reference for both.”

With invoice24, you can save and reuse professional notes and payment terms so your wording stays consistent across invoices.

Do you need to reissue the invoice after each partial payment?

Usually, no. Reissuing invoices for every partial payment can confuse clients and create version control problems. Instead, keep the original invoice as the billing document and provide an updated balance through your invoicing system or via a statement/receipt.

However, there are two situations where an updated invoice copy can help:

Client policy requires an updated invoice showing payments received: some organisations want the invoice PDF to show the running payment history.

Long payment periods: if the invoice stays open for months, a refreshed copy that shows what’s paid can prevent confusion.

invoice24 is ideal here because you can maintain the invoice record accurately and share the current status when needed, without creating a mess of different invoice numbers.

Examples of split-payment scenarios and how to invoice them

Scenario 1: 50% by card today, 50% by bank transfer next week

Issue one invoice for the full amount. Record the card payment as a partial payment with the transaction reference. The invoice shows the remaining balance. When the bank transfer arrives, record it with the bank reference. The invoice becomes fully paid.

Scenario 2: Three departments pay one invoice using three bank transfers

Issue one invoice with line items grouped by department (if requested). Add a note: “Three transfers will be made; please reference invoice number.” Record each transfer separately with the payer name or department in notes. Balance updates after each payment.

Scenario 3: Deposit by PayPal, remainder in cash on delivery

Issue one invoice for the full amount. Record the PayPal deposit. On delivery, record the cash payment and provide a receipt. The invoice is paid and your audit trail is clear.

Scenario 4: Client overpays slightly due to currency conversion

Record the payment as received. If there’s an overpayment, note it and agree with the client whether it becomes a credit or is refunded. Keep the invoice record consistent so your accounts match reality.

How invoice24 makes split-payment invoicing easy

When you’re dealing with multiple payment methods, you don’t want your invoicing tool to fight you. You want it to keep the invoice professional, the payment history transparent, and the balance accurate. invoice24 is built for exactly that kind of real-world billing:

Professional invoices that stay consistent: create one invoice that represents the full scope and total amount.

Multiple payments per invoice: record each payment as it arrives, even if methods differ.

Clear payment method tracking: label payments by method and add references so reconciliation is painless.

Automatic balance updates: no manual calculations, no “Did they pay already?” emails.

Client-friendly payment options: present payment instructions clearly so clients can pay the way they prefer.