How Shopify Payments Works and What Happens to Your Money
What Shopify Payments does
Shopify Payments is a payment processor that lets store owners accept credit cards, debit cards, and digital wallets directly through their Shopify store. When a customer buys something, Shopify Payments collects the money from their card, holds it briefly, then deposits it into the store owner's bank account. You do not need a separate merchant account or payment gateway — it is built into Shopify.
The money does not go straight to your bank. Shopify Payments acts as the middleman: it authorizes the charge, processes it through the card networks (Visa, Mastercard, American Express, Discover), and then moves the funds to you. This process takes a few days, and Shopify takes a percentage of each transaction as its fee.
If you run a Shopify store and want to accept cards without setting up a separate payment processor, Shopify Payments is the default option. It is not a subscription service you add — it is how Shopify handles card payments unless you choose a different processor.
Key Takeaways
- Shopify Payments collects card payments from your customers and deposits the money into your bank account, usually within two to three business days.
- Shopify charges a percentage of each transaction (the rate depends on your plan and the card type) plus a small fee for certain transactions.
- Money is held in Shopify's account temporarily while the transaction clears, then moved to your linked bank account.
- You can see pending deposits, completed deposits, and transaction details in your Shopify admin dashboard under Finances.
- If a customer disputes a charge or requests a refund, Shopify processes that and the money returns to the customer's card or account.
How money moves from customer to your bank account
When a customer enters their card details and completes a purchase, Shopify Payments sends the card information to the card networks (Visa, Mastercard, etc.) to verify the card is valid and has enough funds. This happens in seconds. If approved, the charge is authorized.
The money does not appear in your bank account immediately. Shopify holds the funds in its own account while the transaction settles with the card issuer — this is called the settlement period. During this time, the customer's bank confirms the charge and prepares to send the money. Settlement usually takes one to two business days.
After settlement, Shopify deposits the money into your linked bank account. Most deposits arrive within two to three business days, though weekends and holidays can add time. You can see the status of each deposit in your Shopify admin under Finances > Payouts. The dashboard shows you pending deposits (waiting to settle), completed deposits (on their way to your bank), and the exact date each one should arrive.
Shopify Payments fees and what you pay
Shopify Payments charges you a percentage of each transaction. The exact rate depends on your Shopify plan and the type of card used. Basic plans typically pay around 2.9% + 30¢ per online transaction; higher-tier plans pay lower percentages. American Express often costs more than Visa or Mastercard. Digital wallets like Apple Pay and Google Pay may have different rates than card-present transactions.
These fees are deducted from your deposit before the money reaches your bank account. If a customer spends $100 and you are on a plan charging 2.9% + 30¢, you receive $96.70 and Shopify keeps $3.30. The fee is not charged separately — it is subtracted from the sale amount.
You also pay fees for refunds, chargebacks, and certain other transactions. Refunds are free to process, but if a customer disputes a charge with their bank (a chargeback), Shopify charges a fee (usually $15) to handle the dispute. These fees also come out of your deposits.
Refunds and chargebacks: what happens to the money
If you refund a customer, Shopify sends the money back to their original card or payment method. The refund is processed through the same card networks and usually appears in the customer's account within three to five business days. The refund fee is waived — you do not pay Shopify to issue a refund.
A chargeback is different. It happens when a customer contacts their bank and disputes the charge instead of asking you for a refund. The bank investigates and, if they side with the customer, pulls the money back from your account. Shopify charges you a fee to handle the dispute (typically $15), and you lose both the sale amount and the fee. Chargebacks also hurt your account standing — too many chargebacks can get your store flagged or closed.
You can see refunds and chargebacks in your Shopify admin under Finances > Payouts or in individual order details. Each transaction shows whether it was a sale, refund, or chargeback, and the amount that hit your account.
Linking your bank account and receiving deposits
To use Shopify Payments, you must link a business or personal bank account where deposits will land. Shopify asks for your routing number and account number — the same information you would give an employer for direct deposit. This connection is encrypted and Shopify does not store your full account number after setup.
Deposits are usually made once per day, though the frequency depends on your account history and Shopify's risk assessment. New stores may receive deposits less often (every few days) until they build a track record. You can see your payout schedule in your Shopify admin under Settings > Payments.
If your bank account information changes, you can update it in your Shopify admin. If a deposit fails (for example, if the account is closed), Shopify will retry it and notify you. Repeated failed deposits can suspend your ability to accept payments, so keep your bank information current.
Disputes, holds, and when Shopify freezes your account
Shopify monitors your account for signs of fraud or high-risk activity. If you receive an unusual number of chargebacks, refunds, or complaints, Shopify may place a hold on your deposits. A hold means your money is still deposited, but Shopify delays releasing it to your bank account — sometimes for days or weeks — while they investigate.
In rare cases, Shopify may suspend your account entirely, which stops you from accepting new payments. This usually happens if you violate Shopify's Acceptable Use Policy (selling prohibited items, money laundering, fraud, etc.) or if your chargeback rate becomes too high. If your account is suspended, you lose access to your store and your payment processing stops immediately.
If you believe a hold or suspension is unfair, you can contact Shopify Support to dispute it. Provide documentation of your sales, customer communications, and any evidence that the activity is legitimate. The process can take weeks, and there is no may provide Shopify will reverse the decision.
Shopify Payments versus other payment processors
Shopify Payments is the default, but you can use a different payment processor if you want. Some store owners use Stripe, Square, PayPal, or other gateways because they offer lower fees, different features, or support for payment methods Shopify Payments does not accept.
If you switch processors, you stop using Shopify Payments and your deposits come from the new processor instead. You can have multiple processors active at once, though most stores use one primary processor. Switching does not affect your existing orders or transaction history — Shopify keeps that data in your admin.
The trade-off is complexity: using a separate processor means setting up a merchant account, managing two dashboards, and potentially paying higher fees. Shopify Payments is simpler because it is built in, but it is not always the cheapest option.
Frequently Asked Questions
How long does it take to get money from a sale into my bank account?
Most sales settle within one to two business days, then Shopify deposits the money into your bank account within two to three business days after that. So from the moment a customer buys something to when you see the money in your bank, expect three to five business days. Weekends and holidays add extra time.
What if a customer's card is declined?
If a card is declined, the sale does not go through and no money changes hands. Shopify shows the customer an error message and they can try a different card or payment method. You do not pay any fees for declined transactions.
Can I get deposits more frequently than once a day?
No. Shopify Payments deposits once per day by default, and you cannot change this frequency. New stores or accounts with risk flags may deposit less often. If you need faster access to your money, some alternative processors offer same-day or twice-daily payouts, though they may charge higher fees.
What happens if I close my Shopify store?
When you close your store, Shopify stops accepting new payments immediately. Any pending deposits are still processed and sent to your bank account. You keep access to your transaction history and can download reports for tax or accounting purposes. After 90 days, Shopify deletes transaction data, so download what you need before then.
Do I pay Shopify Payments fees on orders that are refunded?
No. If you refund an order, Shopify does not charge you the transaction fee on that sale. You only pay fees on sales that you keep. However, if a customer disputes a charge (chargeback), you pay a chargeback fee even though you lose the sale amount.