What Are Integrated Payments and What to Consider (2025)

Consumers have an increasingly diverse variety of options when it comes to how and where they spend their money. And your payments technology is a big influence on that decision. Integrated payments create streamlined transactions both on the business and the customer side—making it easier and more convenient to do business. 

Integrated payments allow merchants to accept all kinds of payment methods, which is especially important considering as much as 60% of the global population is expected to use digital wallets by 2026.

So, what exactly is an integrated payment solution, and why does your business need one? Take a look. 

What are integrated payments?

Integrated payments connect payment processing platforms directly with other business systems—like ecommerce platforms, point-of-sale (POS) systems, inventory management, and accounting software—so transactions flow seamlessly across all channels. Rather than relying on disconnected payment solutions, businesses using integrated payments unify their sales, operations, and customer experience into one streamlined system.

Unlike traditional payment processors that operate separately from business systems, integrated payments are built into the commerce platform itself. Shopify is the only platform that offers fully integrated in-person and online payments as part of a unified commerce solution—connecting online and in-person sales, managing inventory in real time, and keeping customer data in one place.

Where are integrated payments used?

Integrated payments streamline transactions across a variety of industries, creating a seamless and efficient experience for both merchants and customers. By connecting payment systems with inventory, sales, and customer data, businesses eliminate friction, improve checkout speed, and gain better visibility into financial performance.

Here’s how integrated payment systems are used in different contexts:

• Retailstores: Brick-and-mortar retailers rely on integrated payments to sync in-store and online sales, manage inventory in real time, and offer flexible fulfillment options like buy online, pick up in-store (BOPIS).
• Ecommercebusinesses: Online retailers use integrated payments to automate checkout, reduce cart abandonment with saved payment methods, and streamline refunds and chargebacks.
• Hospitalityandrestaurants: Hotels, cafes, and restaurants use integrated payments to unify reservations, mobile ordering, tableside payments, and tipping—ensuring fast, convenient service.
• Subscriptionservices: Businesses with recurring billing models use integrated systems for payments to securely store payment details, automate renewals, and reduce failed payments.
• Marketplaces: Multi-vendor platforms leverage integrated payments to simplify transactions, manage payouts, and ensure compliance with financial regulations.

Yutori uses Shopify Payments to manage a variety of payment methods (including pay-later options), ensuring customers—especially students—don’t lose out on timely purchases for limited-edition items. This helped the brand hit 4.3 billion yen (approximately $29 million) in annual sales in just six years.

Benefits of using an integrated payments system

Using an integrated payment system can offer several benefits to your ecommerce business, including:

For businesses

Businesses can benefit in the following ways from using an integrated payment system: 

• Less manual work: Payments automatically sync with inventory, accounting, and customer data, eliminating manual reconciliation and reducing errors.
• A single view of the customer: Unified commerce requires a holistic understanding of each customer. Integrated payments centralize transaction data, making it easier to personalize marketing, loyalty programs, and customer support.
• Efficient cash flow: Payment integration automates invoicing and accounting systems by sending transaction information directly to your general ledger and accounts receivable, allowing you to move money in and out of your company faster than with a manual system.
• Cost savings and reduction of human error: With the right integrated payment processor, you can streamline your accounts receivable and save money in the long run by reducing the number of hours you spend remedying errors.

For customers

• Seamless checkout experience: Whether customers shop online, in-store, or through mobile, integrated payments ensure their preferred payment method works everywhere. Dr. Squatch leveraged Shopify Payments to accept online payments more easily and unlock accelerated payment methods like Shop Pay—now as many as 38% of their customers use it.
• Enhanced security and protection: Built-in security features like payment tokenization and PCI compliance reduce fraud risks and protect customer data.

Alternatives to integrated payments

While integrating payments offers a seamless way to process payments, some businesses may prefer alternative solutions depending on their needs, budget, or existing systems. Here are three common alternatives to integrated payments:

Manual payment processing

For businesses that operate on a small scale or have low transaction volumes, manual payment processing may be a viable option. This method involves manually entering transaction details into a POS system, accounting software, or spreadsheets.

Manual payment processing comes with lower upfront costs since no specialized software is required, plus it allows greater control and flexibility. However, there’s a significantly increased risk of human error, it’s time-consuming, and it doesn’t provide real-time insights into your business.

Hosted payment gateways

A hosted payment gateway is an external checkout solution that processes payments outside of a merchant’s website. Customers are redirected to the payment provider’s page to complete their transaction before being sent back to the merchant’s site.

Examples include PayPal, Stripe Checkout, Authorize.net, and WorldPay. Benefits include a relatively easy setup, lots of payment options, and enhanced security. However, hosted payment gateways lead to disconnected systems. The only true way to take a unified approach to commerce is to handle everything from a single platform, like Shopify. 

Natural Baby Shower, for example, switched from WorldPay to Shopify Payments. This allowed the merchant to enable accelerated payment methods like Apple Pay and Google Pay, plus Shop Pay for a faster checkout and more flexible payment options for their customers. They also tied in flexible installment options like Shop Pay Installments for a simplified and cohesive checkout experience.

Standalone POS and payment systems

Some businesses use separate POS and payment processing systems that aren’t integrated with their ecommerce platform or accounting software. This setup may involve using a third-party card reader or terminal to process transactions independently.

This can be a cost-effective solution for businesses not needing full integration. It also offers the flexibility to choose different providers for payment processing and business management—useful for businesses with complex needs that require specialized POS solutions.

But outside of these special cases, these setups lead to disjointed payment data and systems. They may require manual reconciliation of sales and inventory data, which means more administrative work and potential for reporting inconsistencies. Plus, this approach lacks real-time syncing between sales channels.

How to set up integrated payments with Shopify 

To set up integrated payments with Shopify, you can use Shopify Payments, which is the simplest way to accept payments online. Here’s how you can set it up:

1. From your Shopify admin, go to Settings > Payments.
2. In the Shopify Payments section, click Completeaccountsetup if you haven't set up a credit card payment provider yet.
3. Enter the required details about your store and banking information.
4. If you’re eligible, a Shopify Balance account will be created for you. Otherwise, you’ll need to enter your banking information.
5. Make sure to set up two-step authentication for your account to secure it.
6. Click Save to complete the setup.

Shopify Payments is available in certain countries, so make sure your store operates in a supported region. This setup eliminates the need for a third-party payment provider and integrates seamlessly with your store.