How Do I Set Up Shopify Payments and Avoid Hidden Fees?
How Do I Set Up Shopify Payments and Avoid Hidden Fees?
Q&A Guide to Accept Payments Smartly and Save on Transaction Costs
Q: What Is Shopify Payments?
A: Shopify Payments is Shopify’s built-in payment gateway that allows you to accept major credit cards (Visa, MasterCard, Amex), Apple Pay, Google Pay, and more — without needing a third-party provider like PayPal or Stripe.
Q: Why Should I Use Shopify Payments Instead of Other Gateways?
Top benefits:
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✅ No third-party transaction fees
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✅ Faster payouts directly to your bank
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✅ Seamless integration with your store
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✅ Supports local currencies in multiple countries
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✅ Enables Shop Pay, which increases checkout conversions by up to 1.72x
Q: How Do I Set Up Shopify Payments?
Follow these steps:
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Login to Shopify Admin
→ Go to Settings > Payments -
Choose Shopify Payments
→ Click “Activate Shopify Payments” -
Fill in your business details
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Legal name, address, EIN (for US), PAN/GST (for India)
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Enter bank account details
→ This is where payouts will be sent -
Choose payment methods
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Credit/debit cards, Apple Pay, Google Pay, Shop Pay
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Click Save and you're done ✅
Q: What Are the Fees for Using Shopify Payments?
| Shopify Plan | Credit Card Fee (USA) | Additional Transaction Fee |
|---|---|---|
| Basic | 2.9% + 30¢ | 0% with Shopify Payments |
| Shopify | 2.6% + 30¢ | 0% with Shopify Payments |
| Advanced | 2.4% + 30¢ | 0% with Shopify Payments |
📌 If you don’t use Shopify Payments, Shopify charges up to 2% extra on every transaction. That’s where hidden fees pile up!
Q: What About PayPal or Cash on Delivery? Can I Use Them Too?
Yes! You can use:
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PayPal (default linked to your email)
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Cash on Delivery (COD) for local deliveries
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Razorpay/PayU/CCAvenue (for Indian sellers)
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Stripe, 2Checkout, Authorize.net and others
🧠 Tip: You can combine Shopify Payments + PayPal to offer maximum flexibility to customers.
Q: How Often Will I Get Paid?
Payout schedule varies by country. Example for US:
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Daily payouts
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2–3 day processing time
You can change the payout frequency to daily, weekly, or monthly in settings.
Q: What If Shopify Payments Isn’t Available in My Country?
If Shopify Payments isn’t supported in your country (like some Middle East or African countries), you’ll need to:
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Use a third-party payment provider
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Expect a 1–2% transaction fee from Shopify
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Look for country-specific gateways (e.g., PayFast, Paystack, etc.)
✅ Use Shopify's Payment Gateway Finder to check what’s available in your country.
Q: Tips to Avoid Payment-Related Issues
| Problem | Solution |
|---|---|
| Payments on hold | Complete identity verification early |
| Refunds taking time | Shopify typically processes refunds in 3–5 business days |
| High dispute rates | Use fraud protection tools and be transparent in your policies |
Q: What Is Shop Pay and Why Should I Enable It?
Shop Pay is a fast, secure checkout option exclusive to Shopify stores.
It lets returning customers checkout with one tap, using saved info.
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Boosts conversions by up to 60% on mobile
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Accepts installments (Buy Now, Pay Later) in eligible countries
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Speeds up checkout by storing shipping and payment info securely
✅ Enable Shop Pay under Settings > Payments > Manage Shopify Payments
Conclusion: Smart Payment Setup = Higher Profits & Fewer Headaches
By using Shopify Payments smartly, you can avoid hidden fees, offer faster checkout experiences, and get paid quicker. Whether you're just starting or scaling up, having the right payment system in place is key to business growth.
💰 Need Help Setting Up Payments or GST/Tax Integration?
At RootSyntax, we help Shopify stores launch globally-ready payment systems, including GST setup for Indian merchants. Let’s optimize your checkout →