Accept Partial payments on Draft orders or Manual orders

Payments + Shipping & Fulfilment

Topic summary

Merchants are requesting the ability to accept partial payments (deposits/down payments) on draft orders and manual orders, similar to functionality available in Shopify POS, Square Invoice, and PayPal Invoice.

Core Need:

  • Accept initial deposits (e.g., 50%) when sending draft order invoices to customers
  • Collect remaining balance later via email link or follow-up invoice
  • Properly track partial payments within a single transaction for accounting purposes

Current Limitations:

  • Partial payments work in Shopify POS but not in admin/draft orders
  • Shopify support suggests creating multiple separate draft orders for each payment installment
  • This workaround creates accounting reconciliation issues and inflates transaction counts

Workarounds Mentioned:

  • Opening draft orders through POS on iPad to process partial payments
  • Third-party apps: Wholster, Downapy, Manual Partial Payments
  • Processing deposits outside Shopify (QuickBooks, PayPal) and marking orders as “paid outside of Shopify”

Status:
This remains unresolved despite years of merchant requests. Multiple users express frustration that this “foundational” e-commerce feature hasn’t been prioritized, with some considering switching platforms. The discussion reflects ongoing dissatisfaction with Shopify’s response to what merchants view as basic B2B functionality.

Summarized with AI on November 1. AI used: claude-sonnet-4-5-20250929.
4

Thank you so much for all of this information to help clarify what you’re needing.

Based on what you’re saying the option that would work best for you is to use the Draft Order feature and split the payments up that way. I know it isn’t as intuitive as you’d like, but it will cut out the steps of using square and copying the information over.

If you have your customer’s contact information you can send them an invoice directly from the draft order so that they can pay there, the money is tracked and inventory is adjusted appropriately. The invoice won’t have any information from the previous payment invoice, but you can add that information in the notes.

From the options available in association with what you need I think this would be the best option for you.