Guide · August 2026
Deposits vs BNPL on Shopify — they finance different people
Shop Pay Installments, Klarna and Affirm pay you in full within days and lend to your buyer. A deposit takes part of the price now and leaves the balance for you to collect. Those are different machines solving different problems — and the made-to-order cases where the wrong one gets installed are predictable.
The short version
- BNPL pays you in full. Shop Pay Installments settles within 1–3 business days of capture, and in Shopify’s words you “aren’t at risk if your customers stop making payments” — collecting from the buyer is Affirm’s job.
- A deposit has no financer. You take part of the price now, and the balance is yours to collect — along with the risk of not collecting it.
- The buyer’s cost differs: Affirm’s monthly plans can carry 10%–36% APR. A deposit costs the buyer nothing beyond the price.
- Your cost differs too: Klarna publishes 5.99% + $0.30 per transaction in its own US/Canada merchant annex — Klarna’s direct contract, not the Klarna that arrives through Shopify Payments. A deposit runs through your normal card processing.
- Same store, yes. Same order, no. Shopify’s developer documentation for deferred purchase options charges a deposit’s balance against the payment method vaulted at checkout, and puts that capture on the app — a saved card and a scheduled charge, with no financer in it.
Who is financing whom
Shopify’s own partial-payments page introduces deposits as a way to “offer flexible payment options to your customers” — the same shelf BNPL sits on, which is probably why merchants end up comparing the two as if they were rivals. They are not. Follow the money on one order and the two mechanisms point in opposite directions.
With BNPL, a third party pays you and lends to your buyer. Shopify’s help page for Shop Pay Installments, verbatim: “After you capture the payment for an order placed using Shop Pay Installments, you’ll receive full payment for your order within 1 to 3 business days, excluding the fee incurred for using Shop Pay Installments.” And on risk: “Affirm is responsible for collecting payments from your customers, and you aren’t at risk if your customers stop making payments.” Klarna’s merchant page makes the same two promises in fewer words: “You always get paid upfront and in full with any Klarna payment option” and “We assume credit and fraud risk.”
With a deposit, there is no third party. Shopify’s partial-payments feature — the Plus-only native one — describes the job as letting you “collect deposits or upfront payments”: part of the price at checkout, and the rest an amount you are owed. Even in Shopify’s own B2B checkout, where deposits are native, the deposit “is due up front” and “the remaining balance on the order is due on payment terms” — and Shopify is explicit that the balance does not collect itself: “Payments aren’t automatically captured when the payment terms expire.” Someone has to charge it. You, or an app working for you.
BNPL is a loan to your customer. A deposit is working capital from your customer. One solves the buyer’s problem — affording the price today. The other solves yours — funding a build before it exists, and, in our reading, giving the buyer something at stake if they walk. A store can need both. No store should confuse them.
Side by side, from the documentation
One table, every row read from a named source.
| Question | BNPL | Deposit |
|---|---|---|
| When you get paid | In full, minus the fee. Shop Pay Installments: within 1–3 business days of capturing payment, combined with your regular Shopify Payments payouts. Klarna on Shopify: your next Shopify Payments payout. Affirm through Stripe: up to 2 business days. | In parts. The deposit settles through your gateway at checkout; the balance settles when it is charged later, on the schedule you set. |
| Who finances the gap | The financer. The buyer repays Affirm or Klarna over time, and that debt is the financer's to collect, not yours. | Nobody. The balance is not financed at all — it is an unpaid amount you are owed, waiting for a later charge. |
| Who carries non-payment risk | The financer. Shopify: "you aren't at risk if your customers stop making payments." Klarna: "We assume credit and fraud risk." | You. If the balance charge fails and every retry fails, you hold a part-paid order and the collection problem. |
| What the buyer pays extra | Possibly interest. Affirm's monthly plans run 3 to 36 months and "might include interest" at 10%–36% APR, subject to eligibility. Its interest-free Pay in 4 covers $50–$700 orders only. | Nothing. The price is the price, split in two. |
| What you pay | Shop Pay Installments charges one higher transaction fee that bundles in standard Shopify Payments processing; Shopify doesn't publish the percentage. Klarna publishes 5.99% + $0.30 per transaction ($0.40 CAD) in its own US/Canada merchant annex — Klarna's direct contract, not the Klarna that arrives through Shopify Payments. | Your normal card processing on each charge, plus whatever the deposit app costs. |
| Order size | Shop Pay Installments: $35–$30,000 USD in the US, $35–$30,000 CAD in Canada, £50–£30,000 in the UK. Affirm through Stripe: $35–$30,000 USD. Outside the band, it isn't offered. | No financer's eligibility band. DepositDesk itself sets no cap on order value. |
| Refunds | The fee stays gone: Shopify says the Shop Pay Installments transaction fee isn't returned when you refund, and the same is true of the processing fee on a Klarna order. Klarna through Shopify Payments also allows refunds only within 180 days of the original charge. | Your store's policy call — including whether the deposit is refundable at all. |
| Where it works | Shop Pay Installments: eligible stores in the US, Canada and the UK, with Shopify Payments and Shop Pay both active. Klarna through Shopify Payments: customers in 19 countries, none of which is the United States. Affirm's own Shopify app: one region per store, US or Canada. | Any standard Shopify plan, with a gateway that can store a card: Shopify Payments, PayPal Express, Stripe, or Adyen. |
What BNPL costs, and who pays it
What you pay
Start with the number nobody publishes. Shopify’s help pages tell you that a Shop Pay Installments order carries “a higher transaction fee because it also includes the standard Shopify Payments processing fee” — one bundled fee, not a surcharge stacked on top of your normal rate — but they do not print the percentage. Your rate is in your admin. Third parties commonly cite roughly 5.9% plus $0.30 per transaction; that is an estimate circulating in the ecosystem, not a Shopify number.
Klarna is more forthcoming, though about a different arrangement. Its published standard pricing annex for merchants who contract with Klarna directly in the US and Canada lists 5.99% plus $0.30 USD per transaction ($0.40 CAD) for Klarna Payments — lower rates exist, but they are negotiated individually rather than published. It is Klarna’s own US and Canada merchant contract, not the Klarna that arrives through Shopify Payments, which serves customers in 19 countries and not the United States. Affirm publishes no single rate at all: its merchant pricing is “based on factors including the program option chosen, business size, and the business’s risk profile”, in its own words.
Put the one published rate against a real order. At the 5.99% plus $0.30 in that annex, a $3,000 order costs you $180.00 in fees — that is arithmetic on Klarna’s published direct rate, not a quote. A deposit on the same order runs through your normal card processing, twice, plus whatever your deposit app charges.
That comparison sounds damning for BNPL, and it is not meant to. The fee buys the risk transfer. For roughly six points on Klarna’s published rate you get the whole order value in days, and someone else absorbs the buyer’s default — Stripe’s Affirm documentation adds that Affirm covers losses from customer fraud too. Whether that trade is worth it depends on what you sell, which is the next two sections.
What the buyer pays
Affirm’s Pay in 4 is interest-free and covers orders from $50 to $700. Its monthly plans run 3 to 36 months, “which might include interest”, at rates from 10% to 36% APR subject to eligibility. So on small tickets, BNPL is genuinely free money for the buyer. On a $3,000 commission, the buyer is in monthly-plan territory, where interest is possible rather than excluded — worth knowing before you put the financing badge on a product page whose whole pitch is craftsmanship.
Where BNPL is the wrong tool for made-to-order
None of these is a criticism of BNPL. They are what happens when a tool built for goods that ship this week is pointed at goods that ship in March.
Klarna’s 180-day refund clock
Shopify’s documentation for Klarna through Shopify Payments — the channel that doesn’t serve US customers — says refunds can be processed within 180 days of the initial charge; no cited source gives a window for Shop Pay Installments. Where that clock runs, a made-to-order lead time spends it before the customer has the goods: a six-month build has used essentially the whole window by delivery day. Whatever your own return policy says, the rail that would carry the refund is closed.
Interest lands on exactly your ticket size
The interest-free option is small-ticket: Affirm’s Pay in 4 stops at $700. A typical custom-build ticket lands in Affirm’s monthly plans at 10%–36% APR, so the buyer may be paying a third party for the privilege of buying your work. Those bands are Affirm’s own, read from Stripe’s Affirm documentation — Shop Pay Installments’ own plan structure is not in any documentation cited on this page.
A refund costs you the fee
Mid-build cancellations are the made-to-order failure mode, and BNPL charges you for it: Shopify states the Shop Pay Installments transaction fee is not returned when you issue a refund, and the processing fee on a Klarna order isn’t either. There is also no non-refundable-deposit equivalent inside BNPL — the refund structure is the financer’s, not yours. Our reading, not a quoted rule.
The uncaptured-order question
Shop Pay Installments pays you after you capture the payment. How long an order can sit uncaptured while you build, none of the documentation cited on this page answers. If your lead time runs to months, put that exact question to Shopify support before promising the payment method on a made-to-order product.
And at the edges of the documented bands, the financed option is not there. Shop Pay Installments starts at $35 in the US, $35 CAD in Canada and £50 in the UK, and stops at 30,000 in each market’s own currency; Affirm through Stripe has the same $35–$30,000 limits. Above those ceilings, neither Shop Pay Installments nor Affirm is offered — and no source cited on this page gives a Klarna order-size limit either way. A deposit, or a draft-order deposit raised in the admin, is the split that still exists up there.
Where BNPL is the right tool
Stated just as plainly: if your goods are in stock and ship this week, BNPL is the better tool and a deposit is pointless friction.
- The buyer’s problem is the price, and yours is conversion. BNPL exists precisely for this. A deposit does nothing for affordability — the customer still pays everything, just in two pieces on your schedule.
- You want the cash and none of the collection. Full payment lands in days — 1–3 business days for Shop Pay Installments after capture, up to 2 for Affirm through Stripe, your next payout for Klarna — and there is no second charge to decline. A deposit’s weak spot is exactly that second charge; what happens when the balance charge declines is a page of its own.
- Default and fraud are somebody else’s ledger. “You aren’t at risk if your customers stop making payments” has no equivalent anywhere in deposits. With a deposit, the collection risk on the balance is yours by construction.
The geography footnote, since availability decides this before strategy does: Shop Pay Installments needs an eligible store in the US, Canada or the UK with both Shopify Payments and Shop Pay activated. Klarna through Shopify Payments serves customers in 19 countries, none of which is the United States. Affirm’s own Shopify app takes one region per store, US or Canada. A deposit’s requirement is different in kind: any standard Shopify plan, and a gateway that can store a card for a later charge.
Running both — and the one combination you can’t have
Nothing stops a store offering Shop Pay Installments on its ready-to-ship lines and a deposit option on its made-to-order lines. That is not a compromise; it is the two tools doing the two different jobs they were built for. Pre-orders sit in the same family as deposits — part now, the rest on a schedule — and they get their own treatment on the pre-order deposits page.
Same store, yes. Same order, no. The combination merchants actually ask for — take a deposit now and let the customer finance the balance — has nowhere to sit on a Shopify order. Shopify’s developer documentation for deferred purchase options describes one route for the rest of the money: “a partial amount is charged at checkout, and the remaining balance amount is charged on a specific date … or X days after checkout” against the payment method vaulted at checkout, and “the app is responsible for capturing the remaining balance amount.” A saved card and a scheduled charge — no financer is party to it. Shopify also doesn’t support the express-pay buttons on split payments, so those disappear from checkout when a deposit option is selected. Not financed, not instalments — one balance charge, on the date the plan set. That last step is our reading of the mechanism, not a Shopify statement that BNPL is barred.
If the deposit side is where your made-to-order lines land, the two decisions that matter most are the split and the policy: how much to take now, worked through on the 50% deposit guide, and whether the deposit is refundable, which is a policy question with legal edges covered on the non-refundable deposit policy page. The four ways to take a deposit at all, including the free one, are ranked on taking a deposit on a Shopify custom order.
Which one is yours
- In stock, ships this week, buyers hesitate at the priceBNPL. You get paid in full in days, the financer carries the buyer’s default, and a deposit would add friction while solving nothing.
- Made-to-order, weeks or months of lead time, real cost if the buyer walksA deposit. It funds the build, gives the buyer a stake, and the balance date is yours to set — no financer’s eligibility band, and the refund policy stays yours.
- Ticket above 30,000 in your market’s currencyShop Pay Installments and Affirm both stop there, so the financed option is gone; Klarna’s own order-size limits are in nothing cited here, so ask before you assume. A deposit — at checkout or on a draft order — is the split that still works up there.
- Both kinds of product in one catalogueBoth tools, on different products. They coexist by product line, never on one order.
- The buyer should have skin in the game, not just financingA deposit, with the policy stated up front. BNPL moves the buyer’s payments off your ledger, but the commitment it creates runs to the financer, not to your build. A judgement call, not a rule.
If the deposit side is where you land, this is the part where I tell you what I build. DepositDesk is a $29-a-month flat-rate deposits app for standard Shopify plans, with a 14-day free trial, no per-transaction fee, no revenue share and no cap on order value. Percentage or fixed deposits, with the balance due a set number of days after checkout, on a date, or when you fulfill the order — charged automatically to the card Shopify saved, with retries after 1, 3 and 7 days, an email to the customer each time a charge fails, and the order flagged for you when the ladder runs out.
Its real limits, in the same register as everything above: Online Store channel only — not POS, not B2B, not draft orders. It needs an Online Store 2.0 theme, because the deposit option is a theme app block you add in the theme editor. It needs one of the four vaulting-capable gateways — Shopify Payments, PayPal Express, Stripe, or Adyen. And it is one deposit plus one later balance, not an instalment plan — if instalments are what your buyer needs, that is BNPL’s job. The rest of the deposit-app field is compared on the best Shopify deposit apps.
Questions merchants actually ask
Does BNPL pay the merchant upfront?
Yes — in full, minus the fee. Shopify's wording for Shop Pay Installments: after you capture the payment, you receive full payment for your order within 1 to 3 business days, excluding the fee. Klarna's own claim is blunter: "You always get paid upfront and in full with any Klarna payment option." The buyer's remaining payments are between them and the financer, not you.
Who takes the loss if a BNPL customer stops paying?
The financer. Shopify states that Affirm is responsible for collecting Shop Pay Installments payments and that you aren't at risk if your customers stop making payments; Klarna says it assumes credit and fraud risk. With a deposit there is no financer: you keep the deposit, and an uncollected balance is your loss to chase.
Is a deposit cheaper for the merchant than BNPL?
Usually, but nobody publishes every number. The one published BNPL percentage in this comparison sits in Klarna's own US/Canada merchant pricing annex: 5.99% plus $0.30 per transaction, which is $180.00 on a $3,000 order. That annex is Klarna's direct merchant contract, not the Klarna that arrives through Shopify Payments, which serves customers in 19 countries and not the United States. Shopify doesn't publish the Shop Pay Installments percentage; you see your rate in your admin, and third parties commonly cite around 5.9% plus $0.30, which is an estimate, not documentation. A deposit runs through your normal card processing, plus whatever the deposit app charges. What the BNPL fee buys is the risk transfer.
Can I offer both a deposit option and BNPL on the same Shopify store?
Yes — on different orders. BNPL on ready-to-ship products and a deposit option on made-to-order lines is a coherent setup, not a compromise. What you cannot do is combine them on one order. Shopify's developer documentation for deferred purchase options describes one route for the rest of the money: a partial amount is charged at checkout, and the remaining balance is charged later against the payment method vaulted at checkout — and "the app is responsible for capturing the remaining balance amount." A saved card and a scheduled charge, with no financer party to it. That last step is our reading of the mechanism, not a Shopify statement that BNPL is barred.
Can a customer pay the balance of a deposit order with Klarna or Shop Pay Installments?
No — not in the deposit flow Shopify documents. The remaining balance on a deferred purchase option is charged against the payment method vaulted at checkout, which is the card saved at checkout, and Shopify's developer documentation puts that capture on the app rather than on Shopify. There is no step in that flow where the buyer picks a financer for the balance, and Shopify doesn't support the express-pay buttons on split payments either, so those hide when a deposit option is selected. That is our reading of the mechanism, not a documented exclusion of any named payment method.
What are the BNPL order-size limits?
Shop Pay Installments covers orders from $35 to $30,000 USD in the United States, $35 to $30,000 CAD in Canada, and £50 to £30,000 in the United Kingdom. Affirm's limits through Stripe are the same $35 to $30,000 USD. Affirm's interest-free Pay in 4 option only reaches $700, so larger orders land in Affirm's monthly plans, which can carry 10% to 36% APR — those bands are Affirm's own. Above $30,000, neither Shop Pay Installments nor Affirm is offered. No source cited on this page gives a Klarna order-size limit either way, so ask rather than assume.
Does BNPL make sense for made-to-order goods with long lead times?
Sometimes — but check three things first: whether your lead time fits inside the 180-day refund window Shopify documents for Klarna through Shopify Payments, a channel that doesn't serve US customers and has no published equivalent for Shop Pay Installments; what a mid-build cancellation costs you given that the BNPL fee is not returned when you refund; and whether an Installments order can sit uncaptured for your whole build, which is a question to put to Shopify support before you promise the payment method. A deposit handles long lead times natively, because the balance date is yours to set.
Sources for this page: Shopify’s developer documentation on deferred purchase options, its help-centre pages on Shop Pay Installments — availability, eligibility, getting paid, and its FAQ — and on Klarna as a local payment method in Shopify Payments, its pages on partial payments and B2B payment terms, Stripe’s Affirm documentation, Affirm’s Shopify and merchant documentation, and Klarna’s published pricing annex for US and Canadian merchants — dated September 2023, and still the rate Klarna publishes — all read August 2026. Where a fee is not published, this page says so instead of estimating. If you find something here that is wrong, I would rather hear it: support@depositdesk.app.