
Partial payments on Shopify
Partial payment means several different things. Picking the right one is most of the decision.
At a glance
Four things people mean by partial payment, and who carries the risk in each.
- Deposit, then balance
- You are paid part now, the rest when ready
- Pay-later link
- You are paid when the customer clicks the link
- Buy now, pay later
- You are paid in full now, a lender carries the credit
- Instalments
- Several charges to one saved card over time
- Balance Due does
- Deposit then balance, and the pay-link flow
- Balance Due does not
- BNPL or instalments
The first two are about committing a customer before the goods exist. The third is about spreading the cost of goods that exist now. The fourth is something Shopify reserves for payment apps.
Deposit, then balance
The customer pays part at checkout and the rest later, usually when the item is ready. The card is saved by Shopify (on Shopify Payments or PayPal) and the balance is charged automatically. This is for made-to-order, commissions and pre-orders: anything where you commit resources before the customer has paid in full. It is what Balance Due is built around.
The deposit is a real payment through your own provider on the day of the order. The balance is charged to the same saved card on the date you set or when you mark the order ready, with a reminder three days before and a receipt afterwards.
The four options, side by side
Deposit, then balance
Commitment now, the rest when the item is ready. You carry no credit because the balance is charged before the goods leave, and the order is held until it is.
- Card saved by Shopify at checkout
- Balance charged automatically on your schedule
- Fulfilment held until paid
Pay-later links
The order is placed and a Shopify payment link is sent for the balance, either because the provider cannot charge a saved card or because you want the customer to choose the moment. No automatic charge, so it needs reminders and a hold to work at scale.
- Shopify's own invoice link, any card
- Balance Due runs this flow automatically where a card cannot be vaulted
- Nudges every three days until paid
Buy now, pay later
Shop Pay Installments, Klarna, Clearpay and similar pay you in full at checkout and take the credit risk themselves, for a fee. The customer repays the lender. It is the right tool for ordinary retail where you want the full amount now.
- You are paid in full on day one
- The lender decides who qualifies
- Not a deposit: you cannot charge the rest when the item is ready
Instalments
The same deposit, with the balance split into a schedule of equal payments taken from the saved card. You carry the credit, there is no lender, and you are paid as each charge clears. Shopify treats multi-payment schedules as payment-app territory, so Balance Due does not offer them: it takes a deposit and collects one balance.
- Several automatic charges over months
- Reserved by Shopify for payment apps
- If a customer wants to spread the cost, BNPL at checkout does it without you carrying the credit
How to choose
| You want | Use | Who carries the credit |
|---|---|---|
| Full amount now, customer spreads the cost | BNPL (Shop Pay Installments, Klarna, Clearpay) | The lender |
| Commitment now, rest when the item is ready | Deposit then balance | Nobody, the balance clears before dispatch |
| Commitment now, rest by invoice when you say | Pay link flow | You, until the link is paid |
| Commitment now, rest over months from the same card | A payment app offering instalments | You |
The common mistake is using BNPL as if it were a deposit. It pays you in full on day one, which is good, but it gives you no way to charge the rest when the item is ready, because there is no rest.
Combining them
They are not exclusive. Some combinations are useful.
Deposit plus BNPL
BNPL is a payment method at checkout; a deposit is a purchase option on the product. A customer choosing the deposit option can still pay the deposit itself with any method your provider offers, BNPL included.
Deposit plus pay link
This is the automatic fallback. On a provider that cannot save a card, the deposit is taken at checkout and the balance is collected by link on the due date.
Pay in full plus deposit
Every product with a deposit plan still offers pay in full as the first option. Customers who want to pay everything now can.
What each one costs you
Each charge in a deposit-then-balance flow is a normal Shopify Payments transaction, so you pay the usual processing fee on the deposit and on the balance payment. Balance Due adds no fee of its own on either. BNPL providers charge a higher percentage than card processing in exchange for taking the credit risk and paying you in full at once.
A pay-link balance is charged at your normal rate when the customer pays it. The cost of that route is not in fees, it is in the chasing, which is what the reminders and the hold are for.
A deposit commits the customer. BNPL pays you. They answer different questions, and most made-to-order stores need the first one.
Questions
Can I offer both BNPL and a deposit on the same product?
Yes. BNPL is a payment method at checkout; a deposit is a purchase option on the product. A customer choosing the deposit option can still pay the deposit itself with any method your provider offers.
Does a deposit affect my Shopify Payments fees?
Each charge is a normal Shopify Payments transaction, so you pay the usual processing fee on the deposit and on the balance payment. Balance Due adds no fee of its own.
What if I just want to invoice for the balance?
That is the pay link flow. Balance Due can run it for you with reminders and a hold, or you can send Shopify invoices by hand from the order.
Can Balance Due split the balance into instalments?
No. Shopify treats multi-payment schedules as something only payment apps may offer. Balance Due takes a deposit and collects one balance.
Is a deposit the same as a pre-order?
A pre-order is what you are selling; a deposit is how it is paid for. Balance Due plans are created as pre-order selling plans, so Shopify reserves the units at sale and the deposit and balance follow as on any other order.
Which is best for high-ticket items?
If the item exists now and you want the full amount, BNPL. If the item is made or ordered after the sale, a deposit then the balance, because it commits the customer without you carrying credit.
Does the customer pay interest on a deposit plan?
No. There is no lender, no credit check and no interest. The price is the product price, paid in two parts.
Can the customer pay the balance early?
Yes, from the pay now button on their payment page.
Ready to set one up?
A first deposit plan takes about ten minutes, and the Free plan covers a real order end to end.




