How to Use Authorize.net Instead of Stripe on Shopify
If Stripe or Shopify Payments is holding your funds, delaying payouts, or telling you that your business no longer fits its risk requirements, your first instinct may be to replace it as quickly as possible.
Authorize.net can be a strong alternative, but only when the payment infrastructure behind it is set up correctly.
Authorize.net is primarily a payment gateway. For most merchants using it as an alternative to Stripe or Shopify Payments, it works alongside a separately underwritten merchant account. The gateway sends transactions from your Shopify checkout to the processor connected to that merchant account; the processor and acquiring bank manage settlement and funding.
That separation is the main reason some established, higher-volume, subscription, high-ticket, regulated, or operationally complex businesses choose Authorize.net. Instead of relying entirely on a bundled, self-service payments platform, the merchant can be placed with a processing program that has reviewed the actual business model.
However, changing gateways does not release funds already held by Stripe or Shopify Payments. It does not override Shopify's platform rules, and it does not guarantee that a bank will approve the business. It gives the merchant a different path for processing new transactions after the business, merchant account, gateway, and integration have all been approved and tested.
The short answer
You can use Authorize.net instead of Shopify Payments on an eligible Shopify store by obtaining an Authorize.net gateway connected to a compatible merchant account, installing the Authorize.net payment app in Shopify, connecting the account, testing the complete payment flow, and then activating it for live transactions.
This may be useful when:
Stripe or Shopify Payments has placed a reserve or hold on funds.
Shopify Payments has declined or restricted the payments account.
The business requires underwriting that reflects its products, fulfillment model, ticket size, recurring billing, or chargeback exposure.
The merchant wants its gateway and merchant account relationships to be separate.
A processor or acquiring program that fits the business supports Authorize.net.
It is not a way to avoid underwriting or card-brand rules. Authorize.net, the merchant account provider, Shopify, and the card networks can each have separate requirements.
Do Authorize.net and Stripe integrate with each other?
Usually, no—and that is not the objective of this setup.
Authorize.net and Stripe are separate payment systems. On Shopify, Authorize.net normally replaces Shopify Payments as the primary card-payment provider; it is not installed inside Stripe. Shopify can maintain a secondary gateway in certain legacy subscription-migration scenarios, but that secondary connection is for billing eligible existing contracts—not for routing ordinary new card sales between two providers.
A custom website can be engineered to support more than one payment provider, but that is a payment-orchestration project requiring explicit routing rules, separate token strategies, duplicate-charge protection, reconciliation, and provider approval. It is different from the standard Shopify integration covered here.
Stripe, Shopify Payments, and Authorize.net are not the same thing
Before switching, it helps to separate the products involved.
Stripe is a payments platform that combines payment acceptance, account onboarding, processing, settlement, risk controls, reporting, and developer tools in one ecosystem.
Shopify Payments is Shopify's native payment product. Shopify's official processor list identifies Stripe as a payment processor in many supported countries, but a Shopify Payments account is still managed through Shopify. If Shopify Payments is holding a payout, the merchant must resolve that issue through Shopify—even when Stripe is one of the underlying processors.
Authorize.net is a payment gateway and payments platform. It can be purchased with payment processing or used as a gateway connected to a compatible merchant account. In a traditional setup, Authorize.net handles the secure transaction connection while the merchant account provider, processor, and acquiring bank handle processing approval, settlement, reserves, and funding.
The payment stack at a glance
Storefront and checkout
Both options can work with Shopify or a custom website.
Gateway connection
Stripe or Shopify Payments bundles the gateway into the platform relationship. With a traditional merchant-account setup, Authorize.net provides the gateway connection.
Merchant acceptance
Stripe and Shopify Payments use platform-led onboarding and ongoing risk review. An Authorize.net setup can connect to a separately underwritten merchant account.
Processing and acquiring
Stripe or Shopify Payments manages this within its payment ecosystem. With Authorize.net, transactions are routed to a compatible processor and acquiring bank.
Payouts
Stripe or Shopify Payments manages its own payouts. With Authorize.net, funding is generally managed by the processor or merchant-account provider.
Account support
Stripe and Shopify Payments primarily involve one platform relationship. An Authorize.net setup can involve both the gateway and merchant-services provider.
The Authorize.net route has more moving parts, but that separation can be valuable when the business needs a payment program selected for its actual operating profile.
Why would a business use Authorize.net instead of Stripe?
1. The business can be underwritten before the switch
Fast onboarding is convenient, but an account can still be reviewed after it begins processing. Shopify states that Shopify Payments eligibility is evaluated across the merchant's customer practices, business representation, transaction and dispute management, operating history, and applicable terms.
With a traditional merchant account, the provider can review the business model, website, processing history, financials, fulfillment, ticket size, recurring exposure, refund practices, and projected volume before the account goes live.
That does not eliminate future monitoring. It does create an opportunity to place the merchant with a program that understands what it is approving.
2. The gateway and merchant account can be separate
Stripe generally bundles the gateway, payments account, processing, and risk relationship. Authorize.net can be used as the gateway for a separately underwritten merchant account.
In some gateway-only configurations, a merchant may be able to keep the Authorize.net gateway while changing to another compatible processor. Whether that flexibility exists depends on the gateway ownership, reseller agreement, processor connection, stored data, and technical configuration. Merchants should confirm those details in writing before signing.
3. It can support complex ecommerce operations
Authorize.net can be used for more than a basic online sale. Depending on the platform and configuration, it supports payment authorization and capture, refunds, voids, customer profiles, tokenized stored payment methods, recurring billing, webhooks, fraud controls, virtual-terminal transactions, and developer APIs.
For a custom website, Authorize.net offers several implementation options:
Authorize.net integration options
Native platform payment app
Best for Shopify and other supported ecommerce platforms. This is generally the fastest route because the platform controls most of the checkout experience.
Accept Hosted
Best for a custom website that wants an Authorize.net-hosted payment form. It is designed to reduce PCI scope, and Authorize.net documents it as an SAQ A option.
Accept.js
Best for a custom checkout requiring more design control. Payment information is sent directly to Authorize.net for tokenization. Authorize.net documents the merchant-hosted form option as SAQ A-EP.
Direct API or SDK
Best for complex workflows, software platforms, or specialized payment operations. This route requires experienced development, security review, error handling, and ongoing maintenance.
For Shopify, the native Authorize.net payment app is normally the correct route. A developer should not rebuild the checkout integration unless there is a specific platform-supported reason..
4. Pricing can be evaluated as a complete payment stack
Stripe's flat-rate pricing is simple to understand. A merchant-account setup may offer interchange-plus or another pricing structure, but it can also introduce separate gateway, processor, monthly, per-transaction, batch, compliance, and other account fees.
Shopify may also charge a third-party transaction fee when a store uses Authorize.net instead of Shopify Payments. The rate depends on the Shopify plan and location.
The correct comparison is not “Stripe's rate versus the merchant account rate.” It is:
processing costs + gateway costs + Shopify third-party fees + monthly account costs + chargeback and operational costs
A proposal that looks less expensive at the processor level can be more expensive after the entire stack is included. Compare the projected effective rate using the merchant's actual volume, average ticket, card mix, refund activity, and Shopify plan.
5. The merchant can build around a longer-term payments strategy
A business processing meaningful volume should know who is underwriting it, which entity controls funding, what activity can trigger a reserve, how disputes are managed, who owns the gateway relationship, and what happens if the processor changes.
Authorize.net does not automatically solve those questions. It makes them visible because the gateway and merchant account can be evaluated separately.
When Authorize.net is not the right answer
Authorize.net should not be positioned as a universal high-risk gateway or a guaranteed workaround.
It may not be the right choice when:
The merchant does not have an approved, compatible merchant account.
The products or practices violate Shopify's Acceptable Use Policy, regardless of payment provider.
The business is prohibited by the prospective processor, acquiring bank, card-brand rules, or applicable law.
Shopify does not offer Authorize.net in the merchant's country or region.
The additional Shopify transaction fee makes the total economics unattractive.
The business relies on Shopify Payments features that will be lost after deactivation.
The merchant needs multi-currency functionality or wallet support that the proposed setup cannot provide.
Subscription contracts and stored payment methods have not been evaluated before the switch.
Approval by a merchant account provider does not automatically mean Shopify will permit the business on its platform. Likewise, permission to operate a Shopify store does not guarantee approval for Shopify Payments or another processor. Shopify Payments' terms treat prohibited and restricted payment activity as a separate eligibility issue.
What happens to funds Stripe or Shopify Payments is already holding?
They remain with the provider holding them until that provider releases, applies, or otherwise resolves the balance under its terms.
Stripe's documentation explains that funds placed in a reserve cannot be paid out or transferred until the reserve period is complete. Shopify similarly describes reserved funds as temporarily unavailable until the reserve period ends.
Connecting Authorize.net only changes where eligible future transactions are processed. It does not transfer the old balance, cancel a reserve, or shorten a stated hold period.
If funds are currently held:
Save the reserve or payout notice and every related email.
Export the available balance, payout, transaction, dispute, refund, and reconciliation reports.
Respond to verification or risk-review requests by the stated deadline.
Continue monitoring refunds, disputes, negative balances, and account messages.
Keep the former account and its authorized bank account accessible until all outstanding activity is resolved.
Do not assume that moving new sales ends the merchant's obligations to the former provider.
If the business accepts subscriptions or stores cards with Stripe, a separate data-migration plan may also be required. Stripe can arrange a secure export of eligible customer card data to a qualifying new processor, but Stripe Link credentials are excluded. The receiving provider and the subscription platform must confirm what can be imported before the merchant changes gateways.
Before integrating Authorize.net with Shopify
Do not deactivate the current payment provider first and figure out underwriting afterward. Prepare the replacement payment stack before interrupting checkout.
Step 1: Confirm that the business is eligible for Shopify and the proposed merchant account
Disclose the complete business model during underwriting, including:
Products and services sold
Website and checkout URLs
Monthly and annual volume
Average and maximum ticket
Fulfillment and delivery timeframes
Recurring or subscription billing
Refund and cancellation policies
Processing history
Chargeback and refund history
Marketing channels and claims
Countries served
Related businesses and prior processing accounts
The merchant account must be approved for the business as it actually operates. Misclassifying products, hiding continuity billing, understating volume, or routing transactions through an account approved for a different business creates more risk—not less.
Step 2: Confirm the full payment stack
Before signing, identify each party:
Merchant account provider
Processor
Acquiring bank or sponsor bank, when disclosed
Authorize.net gateway owner or reseller
Shopify payment app
Subscription, fraud, fulfillment, OMS, ERP, or reconciliation apps that touch payments
Ask whether the merchant owns or controls the gateway account, whether the account can connect to another compatible processor later, and who provides support for gateway, funding, disputes, and integration problems.
Step 3: Confirm cost and feature tradeoffs
Review:
Merchant processing pricing
Authorize.net gateway pricing
Shopify third-party transaction fees
Monthly, per-transaction, batch, PCI, chargeback, and optional service fees
Settlement and funding schedule
Reserve terms, if any
Supported currencies
Accepted card brands and wallets
Manual-capture needs
Subscription compatibility
Shopify POS and other sales-channel impact
Deactivating Shopify Payments can remove features that depend on it. Shopify warns that the change can affect Shop Pay, wallets, multi-currency selling, Shopify Balance, Shopify Collective, certain sales channels, and other Shopify Payments-dependent services. A merchant with an outstanding Shopify Capital balance might also be unable to deactivate Shopify Payments until the funding obligation is repaid.
Step 4: Plan subscriptions and stored payment methods before cutover
Shopify currently lists Authorize.net as a supported gateway for subscription products. That does not mean every existing subscription can be moved automatically.
For Shopify subscriptions, payment details are stored in Shopify's vault. Existing contracts, legacy gateways, token migrations, and third-party subscription apps can require a separate migration process. Shopify advises merchants to contact Shopify Support or their Customer Success Manager for setup-specific guidance.
Shopify also states that, for subscription purchases using Authorize.net, PayPal is the only supported wallet option; Apple Pay and Google Pay are not supported for those subscription transactions.
Do not switch a live subscription business until the subscription app, Shopify, the merchant account provider, and the gateway have confirmed the migration path.
Step-by-step: How to connect Authorize.net to Shopify
Shopify's menus change over time and can vary by country, plan, and account status. The current documented Authorize.net workflow is below.
Step 1: Obtain the approved merchant account and Authorize.net gateway
The gateway must be configured for the approved merchant account and a processor connection that supports the required transaction types.
Confirm that you have:
Access to the Authorize.net Merchant Interface
The correct production account
The credentials or authorization required by the Shopify payment app
Funding and settlement information
A support contact for the merchant account and gateway
Treat gateway credentials as sensitive. Do not email them unnecessarily, paste them into support chats, or store them in a public project-management system.
Step 2: Set up a separate Authorize.net sandbox for testing
Authorize.net offers sandbox accounts for test transactions. Shopify's current setup permits the Authorize.net payment app to use sandbox credentials when Use test mode is selected in Shopify.
Keep the environments separate:
Sandbox credentials belong in Shopify test mode.
Production credentials belong in the live connection.
A live Authorize.net account's internal test mode must be turned off before it can accept real transactions.
Never use a real card number in the sandbox.
Step 3: Review uncaptured orders and active checkout dependencies
Before deactivating Shopify Payments or Stripe:
Capture or void any outstanding authorizations as appropriate.
Check pending refunds and disputes.
Review subscription renewals scheduled during the cutover.
Pause automated fulfillment if test orders could trigger it.
Record the current payment settings.
Confirm that staff have access to both payment dashboards.
Schedule the cutover during a lower-volume period when the team can test immediately.
Step 4: Open Shopify's payment settings
From Shopify Admin, go to:
Settings → Payments
If Shopify Payments is active:
Click Manage in the Shopify Payments section.
Click Manage payment methods.
Click Deactivate Shopify Payments.
Click See all other providers.
If Shopify Payments is not active, click See all other providers. If Shopify Payments is unavailable in the store's country, Shopify may instead display Choose a provider.
Step 5: Install and connect Authorize.net
Select Authorize.net from the payment-provider list.
Click Install.
Click Connect to Authorize.net.
Enter the requested Authorize.net credentials or complete the authorization prompt.
Click Activate.
Click Save.
If Authorize.net does not appear, confirm that it is available for the store's country or region and that the business has access to the current Authorize.net payment app.
Step 6: Enable Shopify test mode with sandbox credentials
In Shopify:
Return to Settings → Payments.
In the Authorize.net section, click Edit.
Select Use test mode.
Enter the Authorize.net sandbox credentials.
Click Save.
Use Authorize.net's published test card numbers to place test orders. Do not fulfill test orders or purchase live shipping labels.
Step 7: Test the entire order lifecycle
A successful authorization is not enough. Test the workflows the business actually uses.
At minimum, verify:
Successful authorization and capture
Declined transaction
AVS or CVV response handling
Automatic or manual capture, as configured
Void before settlement
Full refund after settlement
Partial refund, if used
Order cancellation
Mobile checkout
Email confirmations
Taxes, discounts, shipping, and fulfillment
Fraud-rule behavior
Subscription signup and renewal, if applicable
OMS, ERP, fulfillment, accounting, and reconciliation apps
Transaction visibility in both Shopify and Authorize.net
Authorize.net's current Shopify plugin documentation says Shopify's Payment ID is used as the primary identifier and passed to Authorize.net as a reference. Any third-party application that previously relied on an Authorize.net transaction ID for capture, fulfillment, subscriptions, or order management should be tested and updated if necessary.
The same documentation warns that the Shopify plugin may provide limited data for some Authorize.net fraud decisions. Review the fraud settings with the merchant account provider instead of copying rules from another integration.
Step 8: Move from sandbox to production
After testing:
Turn off Use test mode in Shopify.
Connect or confirm the production Authorize.net account.
Verify that the live Authorize.net account is not in its internal test mode.
Place a small live transaction using an authorized company card.
Confirm the order in Shopify and the transaction in Authorize.net.
Void or refund the transaction according to the test plan.
Confirm settlement and the first processor deposit.
Do not assume the integration is complete until the transaction can be traced from Shopify order to gateway record to settlement and bank deposit.
Step 9: Monitor the first 30 days
During the first month, monitor:
Authorization and decline rates
AVS and CVV responses
Fraud-filter holds
Refund and void failures
Duplicate transactions
Subscription rebills
Settlement batches
Processor deposits
Shopify third-party fees
Chargebacks and alerts
Customer complaints
Actual effective processing cost
Keep the old Stripe or Shopify Payments account accessible for historic refunds, disputes, reporting, held funds, and reconciliation.
Common mistakes to avoid
Treating Authorize.net as the merchant account
The gateway is only one layer. The processor and acquiring relationship behind it determine whether the account is approved, how transactions are settled, and when funds are deposited.
Switching before underwriting is complete
Deactivating the current provider before the replacement account is approved and tested can leave the store unable to accept cards.
Assuming “high-risk friendly” means no restrictions
Every merchant account has underwriting criteria. Approval must match the products, marketing, billing model, volume, and fulfillment practices.
Ignoring Shopify's separate rules
An outside payment provider does not override Shopify's Acceptable Use Policy or other platform terms.
Comparing only the advertised processing rate
Shopify third-party fees and gateway expenses must be included in the effective-rate calculation.
Forgetting subscriptions and stored cards
Tokens do not automatically move from Stripe to Authorize.net. Stripe can support secure exports to qualifying processors, but platform, wallet, and subscription limitations still apply.
Copying fraud filters without testing the available data
An overly aggressive AVS, CVV, velocity, or fraud rule can block legitimate orders. A rule that works in a direct Authorize.net integration may behave differently through a platform payment app.
Authorize.net vs. Stripe: Which is better?
Neither option is automatically better for every merchant.
Stripe or Shopify Payments may be a better fit for a straightforward, eligible business that values fast onboarding, consolidated reporting, broad developer tools, wallet support, and a tightly integrated Shopify experience.
Authorize.net with a separately underwritten merchant account may be a better fit for an established or complex merchant that wants its payment program reviewed before launch, needs a compatible traditional merchant account, or wants more separation between the gateway and processing relationship.
The real decision is not simply Authorize.net versus Stripe. It is whether the complete payment stack fits the merchant's business model, risk profile, platform, transaction flow, economics, and long-term operating needs.
Before you switch, have the entire setup reviewed
If your funds are being held or your Shopify Payments account is under review, moving quickly matters—but moving blindly can create a second problem.
Align Ecommerce can review the business model, processing history, Shopify setup, current reserve or restriction notice, subscription requirements, and projected payment stack before the merchant changes providers.
Request a Free Payment Risk Review
The objective is not merely to connect another gateway. It is to build a payment setup that matches how the business actually operates.
Frequently Asked Questions
Authorize.net, Stripe, and Shopify
These answers address the most common questions merchants ask when considering Authorize.net after a Stripe or Shopify Payments hold, restriction, or eligibility decision.
Can I use Authorize.net if Stripe is holding my funds?
Potentially, yes, for new transactions—if the business is approved for a compatible merchant account and Authorize.net is supported by the ecommerce platform. The new setup will not release, transfer, or accelerate funds already held by Stripe or Shopify Payments.
Is Authorize.net a high-risk payment processor?
Not by itself. Authorize.net is primarily a payment gateway. Whether a higher-risk or restricted business can use it depends on the merchant account provider, processor, acquiring bank, business model, platform rules, card-brand requirements, and applicable law.
Do I need a merchant account to use Authorize.net on Shopify?
You need an approved processing relationship behind the gateway. Authorize.net offers payment processing in some configurations, and merchant service providers can also supply an Authorize.net gateway connected to a compatible merchant account. Complex businesses should confirm underwriting before connecting the gateway.
Does Shopify charge extra for using Authorize.net?
Shopify may charge a third-party transaction fee when a store uses an outside payment provider. The rate depends on the store's plan, location, and current Shopify pricing. This is separate from Authorize.net and merchant-processing fees.
Can I move Stripe subscriptions and saved cards to Authorize.net?
Sometimes, but not automatically. Stripe can securely export eligible customer card data to a qualifying new processor, while Shopify has separate tools and requirements for subscription-contract and token migrations. Stripe Link credentials cannot be exported. Confirm the migration plan with Stripe, Shopify, the subscription app, and the receiving provider before switching.