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How Bookkeep Handles Paypal eChecks In Shopify

Some Shopify orders are paid using PayPal eChecks, which behave differently from standard instant PayPal payments. This article explains what eChecks are, why they appear as pending, and how Bookkeep manages them to keep your accounting accurate.

What Are PayPal eChecks?​

A PayPal eCheck is an electronic funds transfer sent from a customer’s bank account to your PayPal account. Unlike typical PayPal payments—which clear instantly—eChecks require bank processing time.

Why is my payment pending?​

PayPal may send a payment as an eCheck when:

  • The buyer pays directly from a bank account

  • PayPal cannot instantly verify available funds

  • PayPal must process the transfer through traditional banking rails

Processing time: Typically 4–7 business days, not counting weekends or holidays.

How Bookkeep Handles PayPal eCheck Transactions​

Because eChecks are not finalized at the time of order, Bookkeep manages them differently to prevent inaccurate accounting entries.

1. eCheck orders appear as “unpaid” in Bookkeep​

Until the payment clears, Bookkeep treats the eCheck as unpaid.
These orders will appear under the Pending Payments line in your daily entries.

2. Bookkeep tracks the payment until PayPal clears it​

Bookkeep does not record the payment as completed because the funds have not yet transferred.

3. Once the eCheck clears, Bookkeep updates the entry automatically​

When PayPal confirms a successful transfer:

  • The entry is updated to reflect the order from unpaid to paid

  • The payment moves out of the Pending Payments line

  • Bookkeep posts the correct finalized payment amount

This ensures you don’t recognize payments before they actually occur.

Why This Matters​

PayPal eChecks can take several days to process, and treating them as completed payments too early can lead to reconciliation errors.
Bookkeep’s workflow ensures:

  • Pending payments are clearly separated

  • Only cleared payments are recognized in your accounting system

  • No manual adjustments are needed later

If you have further questions about how Bookkeep handles payment timing or specific tender types, our support team is here to assist.