Table Of Contents
Introduction
Running an online store isn’t just about having great products and a slick design – it’s also about how you get paid. Whether you’re just launching your Shopify store or managing steady monthly revenue, understanding the ins and outs of Shopify payments, transaction fees, and finance tools can save you time and help you avoid unpleasant surprises.
Have you ever wondered does Shopify take a percentage of sales? Or been stuck figuring out how to record Shopify sales in QuickBooks? You’re not alone. Financial clarity is essential to maintaining healthy cash flow, proper bookkeeping, and smooth daily operations.
This guide walks you through every essential payment and financial tool Shopify offers. You’ll learn how Shopify Payments works, what fees you should expect, how to integrate third-party options like Afterpay, and how to automate accounting processes with QuickBooks. We’ll also look at how to control your payment options – like turning off PayPal – and help you decide between Shop Pay and Shopify Payments.
Understanding Shopify Payments and Transaction Fees
What Is Shopify Payments?
Shopify Payments is Shopify’s built-in payment processing system. It allows you to accept credit cards, Apple Pay, Google Pay, and Shop Pay without relying on third-party providers.
Why use it?
Enabling Shopify Payments simplifies your setup, reduces third-party transaction fees, and integrates directly into your Shopify dashboard.
Does Shopify Take a Percentage of Sales?
Yes, Shopify charges a percentage of each sale, which varies based on your pricing plan:
| Shopify Plan | Credit Card Rate (Online) | Additional Fee (if not using Shopify Payments) |
| Basic | 2.9% + 30¢ | 2.00% |
| Shopify | 2.6% + 30¢ | 1.00% |
| Advanced | 2.4% + 30¢ | 0.50% |
Example:
If you sell a product for $100 on the Basic plan using Shopify Payments, Shopify will take $2.90 + $0.30 = $3.20 as a fee.
If you use a different gateway (e.g., PayPal), Shopify will add the 2.0% fee on top of whatever the third-party charges.
How to Enable and Configure Shopify Payments
Setting up Shopify Payments is simple and can be done within minutes.
How to Enable Shopify Payments
- Go to Settings > Payments in your Shopify Admin.
- Click Activate Shopify Payments.
- Enter required business and banking details.
- Choose the payment methods you wish to accept.
- Click Complete Setup.
Shopify will handle credit card processing, and payouts typically arrive in your bank within 2–4 business days.
Adjusting Payout Schedules
You can customize how often you receive payouts – daily, weekly, or monthly – depending on your cash flow needs.
Offering Flexible Payments: Adding Afterpay & Shop Pay
Today’s buyers want flexibility. Buy Now, Pay Later (BNPL) services like Afterpay and Shop Pay Installments can improve conversion rates.
How to Add Afterpay to Shopify
- Sign up with Afterpay and get approved.
- Install the Afterpay app from the Shopify App Store.
- Follow the configuration steps in the app.
- Enable it under Settings > Payments > Alternative Payments.
Afterpay typically charges merchants a processing fee ranging from 4%–6%.
Shop Pay vs Shopify
- Shop Pay is a fast, secure checkout option that stores customer payment details. It’s part of Shopify Payments.
- Shopify Payments is the underlying gateway enabling Shop Pay and other methods.
Use case: If you want to offer a fast checkout and accept payments directly, enable both Shopify Payments and Shop Pay.
Managing Third-Party Payment Options
You’re not locked into only Shopify Payments. Some merchants prefer PayPal, Stripe, or other gateways for various reasons.
How to Turn Off PayPal on Shopify
- Go to Settings > Payments.
- Locate the PayPal section.
- Click Deactivate.
- Confirm your decision.
Why turn it off? If you find PayPal fees high or customer support lacking, disabling it can streamline transactions and lower costs.
Using Shopify Cash and Shop Pay Installments
What Is Shopify Cash?
Shopify Cash is a loyalty reward for Shop Pay users. Buyers can earn cashback on purchases, which they can use on future orders with participating merchants.
For merchants: Shopify pays you the full order value – Shopify funds the cashback, not you.
Where it helps: Encourages repeat business and customer retention, particularly during promotions.
Shopify & Accounting: Automation and Integration
Tracking sales, fees, taxes, and refunds manually is time-consuming and error-prone. That’s where accounting integrations like QuickBooks come in.
How to Record Shopify Sales in QuickBooks
You can manually or automatically sync Shopify sales to QuickBooks.
Manual Method:
- Export sales reports from Shopify.
- Import into QuickBooks as journal entries or sales receipts.
Automated Method:
- Use apps like QuickBooks Online by Intuit or A2X.
- Sync orders, refunds, fees, and taxes daily or weekly.
How to Set Up Shopify Automated Accounting
- Choose an accounting app from the Shopify App Store.
- Connect your QuickBooks or Xero account.
- Set data sync frequency.
- Map sales accounts, tax codes, and bank accounts.
- Schedule reconciliations and review reporting regularly.
This setup ensures your books are always up to date without extra work.
Handling Fees, Refunds, and Finance Reports
Keeping track of your actual earnings after processing fees and refunds is key to making informed business decisions.
Fee Transparency
Go to Settings > Payments > View Payouts to see:
- Gross sales
- Refunds
- Processing fees
- Net payouts
Refunds and Adjustments
Refunds are deducted from your next payout. Shopify does not return the original transaction fee on refunded orders.
Tip: Set clear refund policies to avoid excessive costs.
Conclusion
Understanding Shopify’s payment systems, fees, and financial tools is not just about reducing costs – it’s about gaining control and clarity over your store’s financial health. From setting up Shopify Payments to integrating accounting software and offering flexible payment options, each tool helps streamline your operations.
As your business grows, optimizing these systems can directly impact profit margins, customer satisfaction, and long-term scalability. Now that you know how to take full advantage of Shopify’s financial features, you’re better equipped to manage, grow, and thrive.
FAQ Section
Does Shopify take a percentage of each sale?
Yes, Shopify charges a percentage based on your plan and payment gateway. Shopify Payments fees range from 2.4% to 2.9% + 30¢ per transaction.
How do I enable Shopify Payments?
Go to Settings > Payments in your Shopify admin and click “Activate Shopify Payments.” Enter business details and bank information to complete setup.
How do I add Afterpay to my Shopify store?
Install the Afterpay app from the Shopify App Store, connect your Afterpay merchant account, and enable it under alternative payment methods in your settings.
How can I record Shopify sales in QuickBooks?
Use integration apps like QuickBooks Online by Intuit or A2X to sync orders, fees, and refunds automatically into your QuickBooks account.
What’s the difference between Shop Pay and Shopify Payments?
Shopify Payments is the main gateway, while Shop Pay is a fast checkout option within it. Shop Pay offers features like one-click checkout and installment plans.
How do I turn off PayPal on Shopify?
Go to Settings > Payments, find the PayPal section, and click “Deactivate.” Confirm to remove PayPal as a payment option.
How does Shopify Cash work?
Shopify Cash rewards buyers using Shop Pay with cashback. The reward is covered by Shopify, and you as the merchant receive the full payment amount.
How can I automate accounting for my Shopify store?
Install an accounting app like A2X or QuickBooks Online, connect your accounts, map transactions, and set auto-sync to keep books updated without manual input.
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