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Practical guide

Check which PayPal workflow your Shopify store actually uses

Last materially reviewed 2026-09-30

Quick answerIdentify the exact gateway before assuming PayPal is either part of Shopify Payments or a separate reconciliation.
What to know

Avoid the one-rule assumption

Shopify documents payment-provider differences, including PayPal Wallet arrangements in specific Shopify Payments markets. Other PayPal workflows are separate. The name PayPal alone does not establish where settlement evidence or fees will appear. Start with the actual gateway configuration and the provider receiving the money.

What to know

For the separate workflow

Link My Books documents gateway summaries for Shopify sales paid through PayPal and notes that Shopify does not supply the PayPal fees for that workflow. A sales summary therefore should not be mistaken for a complete PayPal-account reconciliation. Check the relevant PayPal evidence for charges and transfers.

What to know

Mixed receipts need care

If the same PayPal account receives Shopify and non-Shopify payments, an automatic rule treating every receipt as Shopify can misclassify the other activity. Link My Books’ bank-rule guidance includes a restriction around that scenario. Identify the population before enabling a rule; convenience is not evidence of a correct mapping.

What to know

Define a usable review

Record gateway type, reporting period, source sales population, separate charges and transfers. In a fictional mixed account, label the unrelated receipt as outside this review rather than forcing it into Shopify totals. Have the responsible bookkeeper approve any rule or clearing-account change. If the workflow remains unclear, keep the existing records and resolve the provider boundary before adding another connector.

Continue when useful

Next: Clearing balances

A nonzero clearing balance needs a dated explanation; it is not automatically a mistake or a reason to zero the account.

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Related guides

Clearing balancesA nonzero clearing balance needs a dated explanation; it is not automatically a mistake or a reason to zero the account.Mapping reviewA mapping change needs an owner, scope and historical-effect check before it touches the books.

Sources used for this page

These records support the facts and comparisons above. Merchant-controlled records are labelled so you can separate product claims from independent evidence.

  1. Shopify PayPal reconciliation — Merchant documentation · help.linkmybooks.com · Merchant-controlled · checked 2026-09-30
  2. Shopify payment providers — Merchant documentation · help.shopify.com · Merchant-controlled · checked 2026-09-30
  3. PayPal bank-rule limitation — Merchant documentation · help.linkmybooks.com · Merchant-controlled · checked 2026-09-30