Guide · August 2026
How to take a deposit on a Shopify custom order — the four methods that actually work
Merchants have been asking this in the Shopify community since at least 2020, and the threads are still open. Here are the four real answers, cheapest first, with the constraint that decides between them stated up front rather than buried: whether your payment gateway can store a card for a later charge.
The short version
- A deposit taken at Shopify checkout through a selling plan produces one order with two payments: the deposit now, and the balance charged later to the card saved at checkout.
- That only works on a gateway that can store a payment method. Shopify names four for deferred purchase options: Shopify Payments, PayPal Express, Adyen on Shopify, and Stripe.
- Shopify does not charge the balance for you. The selling plan records when the balance is due; an app has to schedule the charge and fire it, and has to handle every failure.
- A free method exists and works today on any plan and any gateway: a draft order plus a second invoice you send by hand. It produces two orders and you chase the second payment yourself.
- An authorization hold is not a deposit. Shopify Payments authorizes for 7 days, and the hold is for the full order value rather than the deposit.
Start with your gateway
Every method below except the free one depends on a single capability: can your checkout store the customer’s payment method so it can be charged again later, without the customer present? If it cannot, no app and no setting will collect a balance automatically, and you are choosing between invoices and leaving Shopify.
Shopify publishes two lists, and they are not the same list. The one that governs deposits is the one for deferred purchase options — pre-orders and try-before-you-buy — which reads, in Shopify’s own words: “To use pre-order and TBYB options, merchants need to use one of the following payment gateways: Shopify Payments, PayPal Express, Adyen on Shopify, Stripe, which is only available to some merchants.” Shopify’s separate considerations page for subscriptions lists five, adding Authorize.net.
Deposits follow the deferred list, not the subscriptions list. That distinction is the single most consequential fact on this page, and four published gateway lists in this category contradict each other on it.
| Gateway | Deposits / pre-order / TBYB | Subscriptions | The caveat nobody mentions |
|---|---|---|---|
| Shopify Payments | Listed | Listed | Local payment methods are excluded. Card auto-updater is widely supported in the United States, with international support varying. |
| PayPal Express | Listed | Listed | Needs PayPal Reference Transactions approval, which PayPal can refuse. Not available to merchants in France or the United States. |
| Adyen on Shopify | Listed | Listed | Adyen on Shopify is a Shopify Plus arrangement. |
| Stripe | Listed — “only available to some merchants” | Listed | Shopify's own wording qualifies it. Confirm on your store before you build a process on it. |
| Authorize.net | Not listed | Listed | This is the one real divergence between Shopify's two lists. A store on Authorize.net is documented for subscriptions but not for deferred balances. |
| Everything else | Not listed | Not listed | Manual methods (cash, bank transfer, money order) vault nothing by construction. Amazon Pay appears on neither list and Shopify makes no statement either way. |
Underneath the lists there is a harder ceiling. Shopify’s API models a saved payment method as one of exactly four things: a bank account, a credit card, a PayPal billing agreement, or a Shop Pay agreement. Anything that does not reduce to one of those cannot be charged later, whatever a gateway’s marketing says.
Some payment methods are ruled out by name. Shopify states that “customers can’t use local payment methods for subscriptions, pre-orders and TBYB” — which covers Klarna, iDEAL, Wero, Bancontact, Sofort, MobilePay, Swish, TWINT, BLIK, EPS, Przelewy24, ACH Direct Debit, Multibanco, Meses sin intereses and USDC. Shop Pay Instalments is excluded too. A gift card applies only to the first payment, so a deposit paid entirely with a gift card leaves no card to charge the balance against. In practice Shopify hides the ineligible method at checkout rather than letting you create an order it can never collect.
One gap worth knowing if you are in the United States: PayPal Express is not available to merchants in France or the US, and the US option is PayPal Wallet through Shopify Payments. Shopify doesn’t document whether that supports storing a payment method for a later charge, so treat it as unknown rather than as a yes.
The four methods, ranked by cost
Cheapest first. The first one is free and I would genuinely use it at low volume.
1. A draft order, then a second invoice you send
FreeIn the Shopify admin, create a draft order for the deposit amount and email the customer its invoice. They pay through your normal checkout. When the work is finished, create a second draft order for the balance and email that one too.
It needs no app, no particular plan, and — this is the part the app pages never tell you — no particular gateway. You are taking two ordinary full payments, so a store on Authorize.net, on a local gateway, or on bank transfer can do this today, when none of the automated methods are open to it.
What it actually costs you
- Two orders, not one. Two order numbers, two rows in reporting, and a reconciliation job at month-end. This is precisely the complaint merchants voice in the community threads — one described the result as an accounting nightmare.
- You chase the balance. Nothing is saved. The customer has to open a second email and choose to pay it, and if they don’t, your only recourse is to keep asking.
- No card is stored, ever. A draft order does not create a saved payment method. That is not an app limitation, it is how Shopify works, and it is why no deposit app can bolt automatic collection onto this method.
- It is invisible on your storefront. A customer cannot choose to pay a deposit themselves at 11pm; they have to reach you and wait for an invoice.
- If you record the payment yourself rather than having the customer pay the invoice, Shopify’s documentation notes those manual payments “aren’t captured by Shopify” — you are bookkeeping money you collected some other way.
Use it if: you speak to every custom customer anyway, you take a handful of these a month, and ten minutes of admin per order costs you less than a subscription. That is a real number of businesses, and this is the honest answer for them.
2. Shopify’s own deposits: Plus and B2B
Included, if you have PlusShopify has built deposits three times, and all three are gated.
- Partial payments in the admin — a draft order with payment terms, where you take part of the money now. Requires Shopify Plus.
- Draft-order deposits — shipped 1 July 2026 in API version 2026-07 as
DraftOrderInput.deposit. Shopify Plus only, and percentage only: the deposit input takes a percentage between 1 and 99, with no fixed-amount option. If you want “$500 to start” rather than “25%”, this is not it. - B2B deposits at checkout — added 21 June 2024, set per company location, as a percentage of the subtotal. B2B saves the card, but does not charge it automatically: it is Shopify Payments only, and you charge the stored card by hand when the balance is due.
The trap in mixing these with an app
Deferred purchase options — the mechanism every deposit app uses — cannot be used with B2B, cannot be used through Shopify POS, and cannot be used on draft orders. So the native routes and the app route do not combine. You pick one per sales channel.
Use it if: you are already on Plus, a percentage deposit suits you, and you are content to raise each order in the admin. For B2B specifically, this is the right answer even though the balance charge is manual.
3. An app that stores the card at storefront checkout
A monthly subscriptionThis is the only method where the customer serves themselves and the balance collects itself. It uses Shopify’s deferred purchase options: a selling plan on the product offers a deposit, checkout charges part of the price, and, in Shopify’s words, “Shopify will store a customer’s payment method so that merchants can collect the remaining balance amount without contacting the customer.”
It is available on standard Shopify plans — no Plus. The checkout charge can be a percentage or a fixed amount, which is the one thing it does that native draft-order deposits cannot. And whether inventory is committed when the order is placed or when it is fulfilled is a setting the app chooses, so “is my stock reserved?” has an answer, and the answer is: ask the app which one it sets.
The mechanism, stated plainly
Shopify does not charge the balance. The app does. The selling plan’s balance-charge fields are metadata that describe the schedule; Shopify’s own developer documentation puts the work on the app: “It’s your app’s responsibility to schedule the charge at the right time and automate any process around payment failures.” Shopify also notes that “payment reminders aren’t sent for orders with purchase options such as subscriptions, preorders, or try before you buy”, so every customer email about the balance comes from the app too. Dunning — retries and escalation — is a subscriptions feature, not something you inherit here.
What you give up
- Express wallets and local methods. Apple Pay, Google Pay and Shop Pay are not offered on the deposit option, and the local methods named earlier are excluded outright.
- Refunding the deposit on its own. The clearest published statement is a deposit app’s own documentation rather than Shopify’s: Shopify cannot refund just a deposit or just a future payment. Cancelling the order removes the saved card.
- One deposit, one balance. Not a payment plan. Shopify’s API terms prohibit using these purchase options for instalments, layaways and crowdfunding, and that prohibition — not a missing feature — is why every app in this category gives you exactly one later payment.
- A mixed cart collapses. If an order contains several deferred items with different due dates, the balance is treated as due on the soonest of them.
- A real switching cost. Selling plans are deleted 48 hours after a merchant uninstalls the app that created them. Uninstall on a Friday and the deposit options on your products are gone by Sunday.
- You cannot build this yourself. A custom app created in the Shopify admin cannot use purchase options — the scopes involved are protected and require an app registered in the Partner Dashboard.
Use it if: customers should be able to order a custom piece from your storefront without emailing you first, and you would rather not chase a balance. That is the whole case for it, and it is a good one.
4. Take that part of the business off Shopify
A second system to runWorth saying out loud, because merchants in these threads have already done it. The request that comes up again and again is not for a Shopify feature at all — it is “all I need is for draft orders to function like Square Invoices”. That thread was never answered; three years later another merchant replied that it was now 2026 and they were in the same boat.
Invoicing tools built for deposits do this natively: one document, a deposit line, a balance line, reminders included. If custom work is a small, high-touch corner of an otherwise ordinary catalogue, quoting and taking the deposit there — and only putting the finished sale through Shopify, or not at all — is a legitimate answer rather than a defeat.
What it costs
- The order does not exist in Shopify, so inventory, reporting and customer history live in two places.
- Two sets of fees, two reconciliations, and no single view of a customer who buys both ways.
Use it if: your gateway can’t store a card, your lead times run to many months, or bespoke work is genuinely a different business that happens to share a brand.
A $3,000 custom order, both sides
A 50% deposit on a $3,000 commission, with the balance due 30 days after checkout, taken through method 3 — the storefront deposit with a stored card. $1,500 now, $1,500 later. What each side actually sees:
| Stage | What the customer sees | What you see |
|---|---|---|
| On the product page | Two options: “Pay in full — $3,000.00”, and “Deposit — 50% today, balance in 30 days”, labelled “$1,500.00 due today · $1,500.00 balance later”. Apple Pay, Google Pay and Shop Pay buttons are not offered on the deposit option. | Nothing to do per order. The deposit option comes from a plan attached to that product, and the amounts are calculated by Shopify from the variant price. |
| At checkout | Shopify's own checkout shows the split — the amount due today and the amount due later — and asks for a card. Local payment methods and Shop Pay Instalments are not available on this order. | Nothing. This is Shopify's checkout, not an app's, and the card is stored by Shopify. |
| Deposit paid | $1,500.00 charged. Shopify's order confirmation, plus a note that the remaining $1,500.00 will be charged automatically on the scheduled date. | One order in the admin: $1,500.00 received, $1,500.00 outstanding, with the deposit plan's name on the line item. $1,500.00 settles to your account through your normal gateway payout. |
| Balance due | $1,500.00 charged to the card saved at checkout. No invoice to open, no link to click, no action required. | The same order, now fully paid. Shopify does not send a payment reminder for an order like this and does not fire the charge itself — whatever app you use has to schedule it and fire it. |
| If the balance declines | An email from the store saying the balance could not be collected and that it will be retried. Shopify sends nothing here. | An order still showing $1,500.00 outstanding. Shopify does not retry — retries, customer emails and escalation are the app's job, and how well it does them is the whole difference between deposit apps. |
The same $3,000 order through method 1 looks different in one important way. The customer gets an invoice for $1,500, pays it, and that is order #1041. Thirty days later they get a second invoice for $1,500, and that is order #1042. Two orders, two confirmations, and a $3,000 job that shows up nowhere as a $3,000 job.
One thing an app has to work around, worth knowing when you compare them: Shopify’s Admin API does not expose the deposit-versus-balance split on an order. The line item carries the plan’s name and id and nothing more, so any app reporting on your deposits is recording that split itself from the plan it created.
The two objections from the threads
“Can’t I just authorize the card now and capture later?”
No — and this is the single most common wrong turn in these threads. One merchant put the reason in one line: “the capture window for credit cards is only 7~14 days depending on gateway”. Four separate things break:
- The window is short. Shopify Payments provides an authorization period of 7 days. Shopify’s general wording is that the period “can be between 7 and 30 days (depending on your payment service)”. A custom build does not finish in seven days.
- Extending it is gated. Extended authorizations are Shopify Plus with Shopify Payments only — up to 30 days on Visa, Mastercard and Amex, 10 on Discover and JCB, and Diners and China Union Pay stay at 7 regardless of your plan.
- It costs more. A late manual capture carries an extra 1.75% on Shopify Payments. You can capture part of an authorization, but once you do, that authorization can no longer be voided by any means.
- It holds the wrong amount, against the wrong thing. An authorization ties up the full $3,000 against your customer’s credit while they wait, which is the opposite of what a deposit is for. And expiry is terminal: there is no re-authorization path back to the same hold.
The honest version of the answer: if your lead time is under a week, authorize-now-capture-later is fine and you need nothing else. Past that, it is not a deposit mechanism.
“Do the deposit and the balance arrive as one order or two?”
It depends entirely on the method, and this is where the accounting complaint comes from.
- Deposit at checkout through a selling plan: one order. The deposit and the balance are two payments against the same order, and Shopify tracks the remaining amount as that order’s outstanding total. Nothing duplicates.
- Draft order plus a second invoice: two orders. Separate order numbers, separate confirmations, separate rows everywhere. Merchants describe this as an accounting nightmare, and they are not exaggerating at volume.
On fees, be careful what you believe — including from us. Shopify’s documentation says “the transaction fees apply to each capture”, but it says that about multiple captures on a single authorization, not about a deferred balance charge. No Shopify sentence anywhere states that a deposit balance re-incurs a transaction fee. Shopify doesn’t document this — treat it as unconfirmed and ask your gateway.
One fee that is documented, and that catches stores on Stripe and Adyen: third-party transaction fees apply on all third-party and alternate payment gateways even when Shopify Payments is activated. By plan that is 2% on Basic, 1% on Grow, 0.6% on Advanced and 0.2% on Plus — and since a deposit and a balance bill separately, that fee lands on each.
What Shopify doesn’t document
Four questions matter enormously to made-to-order merchants and have no published answer. Anyone who gives you a confident number for these is guessing.
How far out the balance can be scheduled
There is no documented maximum on the deferral window. For a six- or twelve-month lead time this is the first thing you’d want to know, and Shopify doesn’t say. One vendor claims it is indefinite; that is a vendor claim, not documentation. Test it on your own store.
Tax on the deposit versus the balance
Shopify’s documentation is silent — nothing on the time of supply for VAT, and nothing on what happens if a rate changes between the deposit and the balance. Ask your accountant, not a comparison table.
Whether processing fees come back on a refund
Undocumented for the refunded-deposit case. Since you can’t refund a deposit alone anyway, this usually surfaces as a full cancellation question.
How chargeback liability splits
No published statement on how liability divides between a deposit charge and a balance charge months later, nor on whether the later charge is exempt from strong customer authentication as a merchant-initiated transaction. Assume it is not.
Which one is yours
- Your gateway can’t store a card for laterMethod 1, or method 4. No app changes this, and any app that implies otherwise is selling you a balance it cannot collect.
- You sell B2B, or through POSMethod 2. Deferred purchase options can’t be used with either, so the native B2B deposit is the answer — with a manual balance charge.
- A handful of custom orders a month, and you talk to every buyerMethod 1. It is free, it works today, and the admin overhead is smaller than the subscription.
- Customers should be able to order and pay a deposit themselvesMethod 3. This is the only method that puts a deposit option on your product page and collects the balance without you.
- You’re on Plus, and a percentage deposit raised in the admin is fineMethod 2. You have already paid for it.
If method 3 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 and customer emails when a charge fails.
Its real limits, since the whole point of this page is that you should know them before you install anything: 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 above. And it is one deposit plus one later balance, not an instalment plan — for the API-terms reason given earlier, which applies to every app in this category.
Related: how to take a 50% deposit on Shopify works through the split itself — 50/50 against 30/70, and what to do when the balance charge declines. And our scan of 120 made-to-order storefronts found that 52 of the 54 Shopify stores where the question could be answered offered no deposit option at all.
Questions merchants actually ask
Can I take a deposit on a Shopify custom order without an app?
Yes. Create a draft order for the deposit amount, email the invoice, and create a second draft order for the balance when the work is done. It is free, works on every Shopify plan, and works on any payment gateway. The cost is that it produces two separate orders, and you have to chase the second payment yourself — nothing is saved to charge later.
Do I need Shopify Plus to take a deposit on Shopify?
It depends on the method. Shopify's own partial payments in the admin require Shopify Plus, and so do the native draft-order deposits Shopify shipped on 1 July 2026. A deposit taken at storefront checkout through a deposit app does not require Plus — it uses deferred purchase options, which are available on standard plans.
Which payment gateways support a deposit with an automatic balance charge?
Shopify's documentation for deferred purchase options names four: Shopify Payments, PayPal Express, Adyen on Shopify, and Stripe, which it says is only available to some merchants. Shopify's separate list for subscriptions also includes Authorize.net, but Authorize.net is not on the deferred list. If your gateway cannot store a payment method, no app can charge the balance later.
Is the deposit and the balance one order or two?
One order, if the deposit is taken at checkout through a selling plan: the deposit and the balance are two payments against the same order, and Shopify tracks what is still outstanding on it. Two orders, if you use draft orders and send two invoices. That second case is the source of the accounting complaint merchants raise in the community threads.
Can I authorize the card now and capture the full amount when the order is ready?
Only if the order ships within the authorization window, which Shopify Payments sets at 7 days. An authorization also holds the full order value against the customer's credit rather than the deposit, and once it expires there is no way to re-authorize the same hold. For a lead time measured in weeks or months, it does not work.
How far in the future can a deposit balance be charged?
Shopify doesn't document a maximum. There is no published cap on how far out a deferred balance charge can be scheduled, and any specific claim you read about an unlimited window is a vendor's statement rather than Shopify's. If your lead time runs to six or twelve months, test it on your own store before you promise it to a customer.
Is inventory reserved when a customer pays a deposit?
That is a setting, not a fixed behaviour. A deferred purchase option reserves inventory either when the order is placed or when it is fulfilled, and whichever an app chooses is what your store will do. If it matters to you, ask the app which one it sets.
Can I refund just the deposit?
No. Shopify cannot refund only a deposit or only a future payment — the clearest published statement of that comes from a deposit app's own documentation rather than from Shopify, and I could not find a first-party Shopify sentence on it. Cancelling the order also removes the saved card, so the balance can no longer be charged. Plan your deposit policy around that rather than around a partial refund you cannot make.
Sources for this page: Shopify’s developer documentation on deferred purchase options, its help-centre pages on partial payments, subscription considerations, authorization and capture, and transaction fees, its 2026-07 Admin API reference for draft-order deposits, and open threads in the Shopify Community dated 2020 to 2026. Where Shopify publishes nothing, this page says so instead of estimating. If you find something here that is wrong, I would rather hear it: support@depositdesk.app.