Shopify Partial Payments & Deposits: What Actually Works

If you sell custom, made-to-order, or high-ticket products, one question keeps coming back from customers: can I pay part now and the rest later? Shopify can do this — but the honest answer is that the tool you reach for depends heavily on your plan. This guide maps every real option, what each costs, and which one fits your store, without the marketing gloss.

What Partial Payments Mean on Shopify

People use “partial payments” to describe at least three different jobs. The first is a deposit: the customer pays a percentage now and the balance later — common on custom furniture, custom jewelry, event bookings, custom cakes, or made-to-order goods. A car dealership on Shopify Payments or PayPal Express can take one at checkout through a pre-order app and collect the rest later (car deposits).

The second is splitting one order into multiple recorded payments over time. The third is buy-now-pay-later (BNPL), where a third-party lender pays you in full and the customer repays them. Shopify supports all three, through different mechanisms with very different rules.

Shopify's own definition of its native partial-payments feature captures the first two jobs:

One thing partial payments are not: subscriptions. Collecting a deposit and a balance on a single order is a one-time split, not a recurring charge. If you actually want customers billed on a repeating schedule, that's a different system entirely — see our guide to recurring payments on Shopify.

A rental security deposit is a different job again: a refundable sum held against an item that is coming back, not a first share of the price. Our guide to running a rental business on Shopify covers where that deposit can sit.

Which Mechanism Fits: The Matrix

Seven mechanisms cover every deposit and split-payment need on Shopify. The single column that decides your path is the plan gate — find your row, then jump to its section.

The Plus-Only Native Tools

If you're on Plus, you have the cleanest setup: deposits built directly into the admin, no third-party app. Three related features do the work, and they share one base — a percentage of the order taken now, the balance collected later.

Not on Plus? Jump straight to the routes that fit you.

Deposits on draft orders

A draft order is the invoice you build in your admin for a custom quote, wholesale deal, or phone order — and the one place Shopify will email that invoice to the customer as a payable checkout link. When you create one, you set payment terms — due on receipt, due on fulfillment, a fixed date, or a net term (net 7, 15, 30, 45, 60 or 90) — then click + Require deposit and enter a percentage. Shopify bills that percentage now and leaves the balance for when the term comes due.

The draft order underneath all of this has its own decisions — which of the three routes gets it paid, what happens to stock while it sits, and a currency case that removes the invoice option entirely — and those are covered in our guide to draft orders.

Here is the flow, start to finish, on the Plus plan:

B2B payment terms and deposits

B2B on Plus has its own version. On a company location's order you can set the same net terms — net 7 through net 90 — and add a percentage deposit requirement, for example 20% upfront with the balance on net 30. It's the natural fit for wholesale buyers who expect to order now and pay on terms. If that's your model, our guide to B2B and wholesale on Shopify covers the wider setup.

Routes That Don't Need Plus

Most Shopify stores aren't on Plus, and they can still take deposits. The three routes below cover online pre-orders, a catch-all deposit-app layer, and selling face-to-face — pick by how you sell.

Pre-orders with a deposit

Depending on the pre-order payment option you set, you can collect full, partial, or no payment when the customer places the order. Choose a partial deposit and the amount due at checkout shows in the order summary, with the balance charged later.

Deposit apps compared

If you're not on Plus, or your gateway rules out a pre-order app, a deposit app fills the gap on any plan. These add a deposit or split-payment option at checkout and charge the balance automatically or on a set date. The prices below are listings re-read on 28 September 2026 (ratings: 7 September 2026); app pricing drifts, so confirm the current tiers on each listing.

One difference worth noting: most of these apps run their own parallel checkout logic, while Downpay ties into Shopify's native selling plans and purchase options — useful if you want deposits to behave like a first-class part of the product rather than a bolt-on. For everything else, match the app to your gateway and to how you want the balance collected.

In-person split payments

Selling face-to-face? Shopify POS has a native Split payment feature: from the payment screen you can accept more than one payment method on a single order, and you can retrieve the order later to collect the remaining balance with whatever method the customer chooses. It's how a studio takes a deposit at booking and the rest at pickup. For appointment- and service-based businesses, our guide to bookings and services on Shopify goes deeper on the workflow.

Shop Pay Installments: BNPL, Not a Deposit

Shop Pay Installments is where most “partial payment” confusion lives. From the customer's side it looks like paying in parts. From your side it isn't a deposit at all: after you capture the order, you receive full payment within 1 to 3 business days, and the installment risk sits with the provider, not you.

It's available to eligible stores in the United States, Canada, and the United Kingdom, on orders roughly $35 to $30,000 depending on location.

For the merchant, the appeal is conversion on bigger carts. Shopify's own figures run high — it cites up to 28% fewer abandoned carts on larger purchases and a 50% lift in average order value for one in four merchants — but these are Shopify's own marketing claims, published without a disclosed methodology, so treat them as directional and measure the effect on your own numbers before you count on them.

One Shopify-featured merchant describes the upside on their own store:

The takeaway: if your goal is affordability rather than protecting yourself on a custom build, Installments is usually the better tool — you keep the full payment and the customer gets the flexibility. Reserve real deposits for orders where you need money committed before you start work.

And when the question becomes which pay-over-time stack to run — native Installments or a Klarna, Afterpay, or Affirm app — our Shop Pay Installments vs Klarna, Afterpay & Affirm guide compares those routes by eligibility, fees, payout, and geography; this article stays on deposits.

Which Mechanism Is Yours?

You've seen every mechanism and its gate. Still not sure which is yours? Answer five quick questions about your plan, product, and market for a recommendation you can act on.

The Risk Playbook

Collecting money in parts introduces risks a single upfront charge doesn't. None are dealbreakers, but each deserves a guardrail before you go live. Here are the five to plan for.

The Bottom Line

There's no single “Shopify deposit” button — there's a set of mechanisms gated by your plan, your gateway, and your market. Match the tool to your situation and the whole thing gets simple. Get the plan gate wrong and you'll waste hours hunting for a feature that isn't on your account.

Frequently Asked Questions