Payment reconciliation workflow

Merge Shopify Orders with PayPal Transactions

Use this workflow when you already have Shopify and PayPal exports and want to compare store orders with payment transactions. MergeStudio works with the exported Excel or CSV files; it does not connect to either account.

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Recommended setup

Candidate match fields
  • Shared transaction or order reference
  • Customer email for customer-level analysis
  • Date + amount only as a carefully reviewed compound fallback
Merge mode

Keep Everything is useful for reconciliation because unmatched rows remain visible on both sides.

Matching rules

Start with equivalent numbers and extra-space normalization on. Keep Ignore all spaces off unless you deliberately need it.

How to do it

  1. Export the Shopify orders and PayPal transactions you want to compare.
  2. Add both files, select the real data sheets, and correct the Header row if either export starts with report text.
  3. Choose Keep Everything, then select the columns that represent the same reference in each file. If you use more than one match field, every selected field must agree.
  4. Review live match reach and duplicate warnings before choosing output columns and downloading the workbook.
Email is customer-level, not transaction-level. One customer can have several orders and payments, so email alone can produce many-to-many matches.

Common reconciliation traps

Different IDs

A Shopify order number is not automatically the same as a PayPal transaction ID.

Repeated amounts

Date and amount can repeat and should not be treated as unique without review.

Formatting

Prefixes and punctuation in order references may need cleaning before you merge.

🔒
Normal jobs stay on your device.

Spreadsheet contents are processed in the browser for normal local jobs. Oversized jobs are stopped rather than silently uploaded.

Reconcile the two exports

Preview what matches, keep the gaps visible, and download one Excel file.

Open MergeStudio →

Product names belong to their owners. MergeStudio is not affiliated with Shopify or PayPal. Export layouts can change; confirm your own headers and identifiers.