What Shopify Payments does

Shopify Payments is Shopify's built-in payment processor. When a customer buys from your store, Shopify Payments collects the card information, processes the transaction with the customer's bank, and deposits the money into your bank account. You do not sign a separate contract with a third-party payment company — the system is integrated directly into your Shopify dashboard.

The main difference between Shopify Payments and other payment processors is that Shopify owns the processing step. Instead of paying Shopify a store fee plus a separate processor fee, you pay Shopify one combined rate. This can cost less if you process a high volume, though the per-transaction rate varies by card type and whether the card is present at the time of sale.

Shopify Payments is available in the United States, Canada, the United Kingdom, Australia, and several other countries. If your store is in an unsupported country, you will need to use a different processor like Stripe or Square, which you can still connect to your Shopify store.

Key Takeaways

  • Shopify Payments processes card payments directly through Shopify, so you see transaction details in your Shopify admin without logging into a separate account.
  • Deposits go to your bank account on a rolling basis — usually within one to two business days after a sale, though the exact timing depends on your bank and card network.
  • You pay a percentage of each sale plus a fixed per-transaction fee; the percentage varies by card type (Visa, Mastercard, American Express, Discover) and whether the card is physically present.
  • Shopify Payments holds a small reserve of your money for the first 90 days to cover chargebacks and refunds, then releases it gradually.
  • If a customer disputes a charge, Shopify handles the chargeback process, but you may lose the money and the product if the dispute is ruled against you.

How money moves from your customer to your bank account

When a customer enters their card details on your store, Shopify Payments sends that information to the card network (Visa, Mastercard, American Express, or Discover). The network checks with the customer's bank to confirm the card is valid and the account has enough funds. If approved, the bank holds the money and sends a confirmation back through the network to Shopify.

Shopify then deposits that money into your bank account. The timing depends on your bank's processing speed and the card network's settlement schedule, but most deposits arrive within one to two business days. You can see pending deposits in your Shopify admin under the Finances section — this shows you exactly when Shopify sent the money to your bank, even if your bank has not yet posted it to your account.

If a customer pays by a method other than card — such as Apple Pay, Google Pay, or PayPal — Shopify Payments still processes it, because these methods ultimately pull from a card or bank account behind the scenes. The deposit timeline is the same.

What fees you pay and when

Shopify Payments charges you a percentage of each sale plus a fixed per-transaction fee. The percentage depends on the card type and whether the card is physically present (swiped in person) or entered remotely (online or over the phone). In-person card-present transactions cost less because the fraud risk is lower.

As of this writing, online card-not-present transactions cost 2.9% plus 30 cents per transaction for Visa and Mastercard, and 3.5% plus 30 cents for American Express and Discover. In-person transactions cost 2.7% plus 8 cents. These rates change periodically and vary slightly by country, so check your Shopify admin or the Shopify Payments pricing page for your current rates.

Shopify deducts these fees from each deposit before the money reaches your bank account. You do not pay them separately — they are subtracted automatically. If you issue a refund, Shopify refunds the customer's money and credits back the fees you paid on that transaction.

The reserve hold and how it protects Shopify

When you first start using Shopify Payments, Shopify holds back a portion of your deposits in a reserve account. This reserve typically covers the first 90 days of your store's operation. During this time, Shopify deposits your sales money into the reserve instead of directly to your bank account, releasing it gradually — often in weekly or bi-weekly batches.

The reserve exists to cover chargebacks and refunds. If a customer disputes a charge or you issue a refund, Shopify pulls the money from the reserve rather than from your bank account. This protects Shopify from the risk that you might spend money from a sale before a chargeback comes in weeks later, leaving Shopify unable to recover the funds.

After 90 days, if your store has a low chargeback rate and no major issues, Shopify releases the reserve and deposits your money directly to your bank account on the normal schedule. The exact release date depends on your store's history and Shopify's risk assessment. You can see your reserve balance and release date in your Shopify admin under Finances.

Chargebacks and disputes: what happens when a customer contests a charge

A chargeback occurs when a customer contacts their bank and says they did not authorize a charge or did not receive what they paid for. The bank investigates and either sides with the customer (reversing the charge) or sides with you (the charge stands). Shopify Payments handles the chargeback process on your behalf, but the outcome affects your money directly.

If a chargeback is ruled in the customer's favor, Shopify removes the sale amount from your account — either from your reserve (if you still have one) or from your next deposit. You also lose the product or service you provided. Additionally, Shopify charges you a chargeback fee, which varies by card network but is typically $15 to $25 per dispute.

To reduce chargebacks, use clear product descriptions, confirm orders with email receipts, and respond quickly to customer inquiries. If a customer contacts you about a problem before filing a chargeback, you can often resolve it with a refund or replacement, which costs you less than a chargeback fee.

Deposits, timing, and what to expect in your bank account

Deposits from Shopify Payments appear in your bank account as a single line item, usually labeled something like "SHOPIFY" or "SHOPIFY PAYMENTS." The amount shown is your total sales minus fees and any refunds or chargebacks processed that day. You do not see individual customer transactions in your bank statement — only the net deposit.

If you want to see which individual sales made up a deposit, log into your Shopify admin and go to Finances > Payouts. This page shows every deposit, the date it was sent to your bank, and a breakdown of the sales, fees, and adjustments included in that deposit. You can read this data as a CSV file for your accounting records.

Deposits typically occur once per business day, though the exact timing depends on when Shopify batches your transactions and your bank's processing schedule. Weekends and holidays may delay deposits by a day. If you notice a deposit is missing or late, check your Shopify admin first to confirm Shopify sent it — if it shows as sent but has not arrived at your bank, contact your bank's customer service.

When Shopify Payments is not available or not the right choice

Shopify Payments is not available in all countries. If your store is based outside the supported regions, you will need to use an alternative processor. Shopify supports dozens of third-party processors including Stripe, Square, PayPal, and others. You can add these to your store and they work similarly to Shopify Payments, though you may see separate fees and a separate dashboard.

Even if Shopify Payments is available in your country, it may not be the cheapest option for your business. If you process a very high volume of in-person sales, Square or another processor might offer lower rates. If you sell internationally and need to accept payments in multiple currencies, some third-party processors handle this more smoothly. Compare the total fees across processors for your specific sales mix before deciding.

Some businesses use multiple processors at once — for example, Shopify Payments for online sales and Square for in-person sales at a pop-up or market. This is allowed and can make sense if different channels have different fee structures.

Frequently Asked Questions

How long does it take money to show up in my bank account after a customer buys something?

Shopify usually sends the deposit to your bank within one to two business days. Your bank may take an additional day to post it to your account, so the total time is typically two to three business days. During the first 90 days, money goes into a reserve and is released on a schedule set by Shopify, which may be slower. You can see the exact date Shopify sent each deposit in your Shopify admin under Finances > Payouts.

What happens if a customer uses a stolen card to buy from my store?

If the cardholder later disputes the charge, Shopify will reverse it and you lose both the money and the product. You are also charged a chargeback fee. To reduce this risk, use Shopify's built-in fraud tools, which flag suspicious orders based on address mismatches and other signals. You can also require customers to enter the CVV code on the back of the card, which adds a layer of verification.

Can I use Shopify Payments if I have had chargebacks in the past?

Yes, but Shopify may hold a larger reserve or require a longer reserve period if your account shows a high chargeback rate. If your chargeback rate exceeds Shopify's threshold (typically around 1% of transactions), Shopify may suspend Shopify Payments and require you to use a different processor. Keeping your chargeback rate low by providing good customer service and clear product information helps you avoid this.

Do I pay Shopify Payments fees on refunds I issue?

No. When you issue a refund, Shopify refunds the customer's money and credits back the processing fees you paid on that transaction. So if a customer paid $100 and you charged $2.90 in fees, you get back the $2.90 when you refund the $100.

What if my bank account information changes — do I need to update it in Shopify?

Yes. Go to Settings > Payments in your Shopify admin and update your bank account details. Shopify will verify the new account with a small test deposit before sending full deposits to it. If you do not update your account and Shopify tries to deposit to a closed or incorrect account, the deposit will fail and your money will be held until you provide correct information.