Shopify doesn’t have a native “deposit” option in standard payment settings - but there are three methods that actually work to take a partial payment on a Shopify order: draft orders with manual invoicing (works on every plan, no app needed), deposit apps from the Shopify App Store (the most common path for stores doing this regularly), and custom checkout extensibility for Shopify Plus stores. This guide covers each method, when to use which one, and the common pitfalls to avoid.

Key Takeaways
1
There is no native “Split Payment” option in Shopify’s standard payment settings - anyone who claims otherwise is describing functionality that doesn’t exist on Shopify in 2026.
2
The simplest deposit method on any Shopify plan: draft orders, where you charge the deposit amount manually and invoice the balance later.
3
For repeat or scaled use, deposit apps like Partial.ly, Downpay, and Shopify Subscriptions handle the full deposit-then-balance flow automatically.
4
Shopify Plus stores can build native deposit fields directly into checkout using checkout extensibility - most flexibility, but requires development work.
5
Tax, refund, and chargeback handling are the most common failure points when collecting deposits - plan for them before launching the workflow.

Method 1: Draft Orders With Manual Partial Payment

The simplest method, available on every Shopify plan. Use this for one-off deposits - custom orders, services, low-volume rentals, or B2B quotes.

  1. In your Shopify admin, go to Orders > Drafts and click Create order.
  2. Add the products or a custom item, set the line-item price to the deposit amount you want to collect now (e.g., 30% of the full price as a single line “Deposit on Custom Order #1234”).
  3. Add the customer and any notes about the balance owed.
  4. Click Send invoice - Shopify emails the customer a payment link.
  5. When the customer pays, the draft becomes a paid order in your system.
  6. For the balance, create a second draft order for the remaining amount, reference the original deposit in the notes, and send another invoice.

When this works: low volume, custom or service-based orders, B2B with negotiated terms, rental businesses where the deposit and the balance are days or weeks apart.

Where it breaks: if you’re processing dozens of deposit orders a month, manually creating two draft orders per customer becomes painful. At that point, move to Method 2.

Method 2: Deposit Apps from the Shopify App Store

For stores doing deposits regularly, dedicated apps automate the full deposit-then-balance flow. The most common options as of 2026:

  • Partial.ly Payment Plans - handles deposits + scheduled balance payments. Customer pays the deposit at checkout, then Partial.ly auto-charges the balance on the schedule you set. Works for both one-time deposits and full installment plans.
  • Downpay - Shopify-native deposit-and-balance app. Set a deposit percentage on individual products or collections. Customer pays the deposit at checkout, gets a payment link for the balance later.
  • Shopify Subscriptions - Shopify’s first-party app, free, supports split-payment configurations. Useful when your “deposit” is part of a recurring or pre-paid plan.
  • Splitit, Sezzle, Affirm, Klarna - buy-now-pay-later providers. Different model from a traditional deposit (the customer pays you in full, the BNPL provider charges them in installments) but solves the same customer-facing problem of “I don’t want to pay the full amount today.”
  • Pre-Order Manager apps - for products shipping later. Many include a deposit option (charge a percentage now, balance when item ships).

How to choose: if you want the deposit logic baked into the storefront and customers paying the deposit at the moment of checkout, use Partial.ly or Downpay. If you’re already running subscriptions or pre-orders, look at the deposit options inside those apps before adding a separate one. If your customers are price-sensitive and “deposit” is really “split into payments,” BNPL is often easier than a deposit app.

Method 3: Shopify Plus Checkout Extensibility

Stores on Shopify Plus can build a native deposit field directly into checkout using checkout extensibility (the modern replacement for checkout.liquid customization). This is the most flexible option - fully integrated, no app dependencies, full control over UI - but it requires development work.

Typical Plus deposit implementations:

  • Customer toggles “Pay deposit only” at checkout.
  • Checkout calculates and charges the deposit amount.
  • A custom flow stores the balance amount and customer info, then sends a balance-due payment link via Shopify Flow or a custom integration on a scheduled trigger.
  • Order metafields track deposit status, balance due, and balance-paid date for accounting.

This is overkill for most stores. It pays off for high-volume Plus merchants where a deposit app’s per-transaction fees would exceed the cost of the development. Consult a Shopify Plus partner agency if this is the path that fits.

When You Want to Take a Deposit (Use Cases)

Deposits make sense in a handful of distinct scenarios:

  • Custom or made-to-order products. Deposit to lock in the order, balance when the product ships.
  • Service businesses. Deposit to confirm the booking, balance after delivery.
  • Rental businesses. Deposit covers potential damage; can be refunded after return inspection.
  • High-ticket B2B. Deposit confirms commitment before you commit production capacity or supplier orders.
  • Pre-orders. Charge a deposit now (or fully process the order with a delayed-fulfillment timer), balance when ready to ship.
  • Event tickets and reservations. Deposit holds the spot; balance due before the event.

Common Pitfalls (Plan for These Before Launching)

  • Tax handling. Whether you collect tax on the deposit or only on the balance varies by jurisdiction. Most Shopify deposit apps default to collecting prorated tax on the deposit, but check with your accountant. Misallocating tax across the two payments creates compliance headaches.
  • Failed balance payments. Customer pays the deposit, then disappears or their card declines on the balance. Decide your policy in advance: do you keep the deposit, refund it after a deadline, or try to recover the product? Document the policy on your storefront before customers commit.
  • Chargebacks on deposit-only orders. If a customer disputes the deposit charge, you can lose the deposit AND the chargeback fee. Use clear product descriptions stating the deposit terms, and require explicit acknowledgment at checkout (a checkbox or terms link).
  • Accounting reconciliation. Two payments per order doubles your accounting work unless you wire it up correctly. Most deposit apps export a combined order record to accounting tools (QuickBooks, Xero) - verify your app does this before scaling.
  • Inventory holding. A deposit-paid order should reserve the inventory. Most deposit apps integrate with Shopify’s native inventory; check this if you sell physical goods. For custom or made-to-order, the deposit is what triggers production, so the inventory question is moot.
  • Refund flows. If a customer cancels after the deposit, the refund should be straightforward - through the original payment. If they cancel after the balance, refunding both transactions is two operations. Practice the refund flow in your test store before going live.

What About Shopify Finances?

Shopify’s Finances dashboard tracks all order revenue but doesn’t natively split deposit-vs-balance accounting. If you’re running deposits at any scale, you’ll likely want a deposit app that exports to your accounting system, or build a custom report through Shopify’s GraphQL Admin API to separate deposit revenue from balance revenue. For most small stores, the deposit app’s own dashboard is enough.

For stores running deposits alongside other unconventional payment flows (offline payments, COD, manual invoicing), our guide on Shopify payment apps covers the full ecosystem. If you’re considering simplifying the broader checkout flow, see simplifying checkout with Shopify apps, and for processor-level questions, can you use Stripe with Shopify covers when Stripe is the right call.