Software that can track shopify payments, shopify fees on those payment and refunds using Shopify

Shopify Discussion
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Topic summary

Main issue: A merchant cannot reconcile the Shopify 1099 with their books. They need separate figures for Shop Pay (Shopify’s checkout) including gross payments, Shopify fees on those payments, and refunds, but note Shopify’s built-in reports mix Shop Pay and PayPal.

Requests (clarity needed):

  • Gross Shop Pay payments for the year.
  • Shopify fees tied to those payments.
  • Refunds on Shopify Payments transactions.

Proposed solutions:

  • Report Pundit: Offers a Payments & Transactions report showing gross Shop Pay transactions for any date range, Shopify fees by order, and payments/refunds per order. Can also track payouts from Shop Pay, PayPal, Stripe, Klarna, and Sezzle. Support via live chat/email; used by merchants to match payouts.
  • Better Reports: Provides payout reports with transactions, fees, and net payout amounts, either detailed per order or summarized by payout date. Includes 60+ built-in reports, scheduling to email/Google Drive, and exports (CSV/Excel/PDF). 14-day free trial.

Status/outcome: No confirmation of a fix. Recommended next step is to test the third‑party reporting apps to isolate Shop Pay vs PayPal data and reconcile with the 1099. Discussion remains open.

Summarized with AI on December 11. AI used: gpt-5.
1

This is my second year using shopify and last year regardless of what me and my accountant did we were not able to match the 1099 from Shopify. Paypal has been a lot easier with the monthly statements when it comes to payment received, returns and paypal fees.

I am looking for help to see the following items:

  1. Gross payment for the transactions that used shop pay for the year.

  2. Shopify fees on those payments.

  3. Refunds done on the transactions done on the shopify payments.

THe reporting I saw on shopify mixes shopify and paypal payments.

2

@Tral ,

With Report Pundit’s Payments and Transactions Report:

  1. We can show all the gross payment transactions that have occurred through Shop Pay for any selected date range.
  2. You can see the Shopify fees for payments based on the order name.
  3. Check payments and refunds for each order number within any selected date range.
    Many Shopify merchants use Report Pundit to match payouts. For more information, you can contact our support team through live chat or email.

Additionally, Report Pundit’s custom reporting options enable you to track payouts from platforms like Shop Pay, PayPal, Stripe, Klarna, and Sezzle.

Thanks,
Report Pundit Team

3

Hi @Tral

Claudia here from Better Reports.

I would recommend our app Better Reports for this.

We offer a couple of built-in payout report that displays Shopify transactions, including transaction fees and net payout amounts. One version of the report provides all the order details, while another offers a summary organized by payout date.

In addition, Better Reports includes 60+ built-in reports covering common merchant use cases. You can also schedule reports to run at set intervals, delivering them directly to your email or Google Drive. Reports can be exported in CSV, Excel, or PDF formats.

I encourage you to install Better Reports and start your free 14-day trial.

What do you think?