Integrated PaymentsHow Integrated Processing Benefits Both Merchants & Consumers

Shelley Palmer | June 5, 2025 | 9 min read

This featured video was created using artificial intelligence. The article, however, was written and edited by actual payment experts.

What are Integrated Payments?

In a Nutshell

Want to get paid faster for credit card orders? Like to offer your customers more payment options? An integrated payment processing solution can automatically enter and reconcile your invoices as you receive them, and balance your general ledger in real-time. Particularly for online merchants, it can be a game-changer, providing a safer and easier customer experience that can help reduce chargebacks and fraud.

Curious About Integrated Payment Solutions? Here’s What to Look for.

Imagine that you could key-in information once, then automatically use wherever or however else it’s needed, eliminating the possibility of re-entry mistakes. As long as the data is entered correctly from the start, the numbers are always accurate, even across multiple related databases.

That’s the basic idea behind integrated payments.

The integrated payments concept lets you take credit card information obtained during a transaction and forward it to other accounting programs for processing and posting. It sounds great... but does it work? In this post, we look at how an integrated payments system can benefit your business.

What is an Integrated Payment System?

Integrated Payments

[noun]/in • tuh • gray • tuhd • pay • muhnts/

An integrated payment system is an automated payment processing platform. It takes transaction data from the point of sale, sharing information directly with other connected systems without manual input.

As an eCommerce merchant, you’ll need a lot of different services in your tech stack. We’re talking payment processing services, an accounting system to track transactions and profitability, an order management system to track inventory and purchases, a customer relationship management (CRM) system to track customers, an online storefront for customers to shop and checkout from… and more.

Traditionally, your payment processor, accounting system, order management system, CRM, and website aren’t integrated; they don’t sync up or talk to each other. This is fine if you’re running a small operation, but it quickly becomes a problem when you serve thousands of customers and need to track tens of thousands of orders.

That’s where integrated payments come in.

It’s a strategy to closely link together all of your information systems. It helps prevent duplicate or out-of-date data, sidestep manual importing and exporting, and ensure that every transaction submitted for processing is seamlessly and accurately reflected in your accounting software, order management system, and CRM.

Important!

This is especially relevant to merchants who might otherwise need to manually copy, or even key-in numbers. Payment information comes straight from the online checkout, and is automatically used to process and post payments to the associated transaction or invoice.

What Are the Benefits of an Integrated Payments Model?

The immediate advantage here is streamlined operations. Through integration, payments are posted and ledgers are updated at the time of sale. But, there are a few other long-term benefits to an integrated approach that you should consider, too:

Higher Customer Satisfaction

Non-integrated payments often lead to checkout friction, frustrated customers, and cart abandonment. Integration makes the process smoother, faster, and more secure, helping reduce churn while enhancing the shopping experience.

More Efficient Accounting

Manual data entry, review, and reconciling are both tedious and time-consuming. By eliminating these tasks, integrated payment processing allows the merchant to better allocate staff and resources to grow the business.

More Accurate Recordkeeping

Integrated systems remove the manual entry — and re-entry — of data from the process. This effectively eliminates accounting discrepancies, reconciliation mistakes, and revenue-reporting errors. The same information is automatically available to all systems at the same time.

Faster Payouts

With credit cards, there’s a time lag between making the sale and receiving the funds. Integrated payments systems deliver immediate posting, helping merchants get paid as quickly as possible.

More Customer Payment Options

Most integrated payments solutions work with multiple payment channels (credit or debit cards, mobile payments, gift cards, etc.), allowing merchants to offer customers more payment options. Also, services such as PayPal can be used without requiring the buyer to exit to the PayPal site.

Recurring Payment Processing

Subscription billing is easier using integrated payments, especially if the system is also connected to the merchant’s customer relationship management (CRM) software. Customers only have to provide payment information once. After that, it can be stored and used to automate future invoicing and process ongoing payments.

In-Depth Analytics

A sophisticated payments system that is integrated across processes can provide deeper metrics for business performance. The merchant should be able to analyze historical revenue data and judge the business’ performance by channel, time frame, location, and more.

Fraud & Chargeback Oversight

Integrated payment solutions record all sales, potentially allowing merchants to spot trends or patterns indicating possible fraud. Shared data can also simplify data retrieval in the event of a customer dispute.

Increased Data Security

Manual accounting can often compromise data security. Instead of storing information on-site, integrated payment processing allows merchants to leverage cloud-based accounting, which runs on off-site servers. An accounting program compliant with the Payment Card Industry Data Security Standard (PCI DSS) helps protect credit card information in the event of a data breach.

Non-IntegratedIntegrated
Multiple Programs & Systems: Standalone systems don’t connect to your POS, meaning you’ll need at least two (and usually more) processing systems.Everything Together: Integrated payment systems connect directly with your POS and transfer data without needing a third-party processor.
Multiple Entry Points: Manually keying in the same information in multiple locations is not only tedious, it increases the odds of a mistyped entry.One Entry Point: Data received directly from the POS and used consistently by the entire system dramatically lowers the odds of entry mistakes.
On-Site Data Storage: There is always the risk of data theft or fraud. If you’re storing personal customer information, you’re responsible for going through all the necessary steps to keep it safe.Integrated Storage: Integrated payment systems are required to comply with PCI DSS regulations, which are global standards for data security and loss protection.

Use Cases for Integrated Payments

Integrating your payments system with your other information systems can help you eliminate errors inherent in manual data entry and migration. It also saves you time and hassle.

Take Shopify, for example. Its flagship product is its eCommerce platform, which allows you to build a website, list products for sale, and direct customers to checkout.

Shopify Payments is tightly integrated within the Shopify ecosystem. This is the company’s payment provider, which lets you accept all major credit and debit cards on a one-time or subscription billing basis. It eliminates “the hassle of setting up a third-party payment provider or merchant account and having to enter the credentials into Shopify.”

In the past, an eCommerce store wasn’t so easy to set up. You’d have to sign up for a website hosting service, build a website yourself, design a checkout flow, sign up for a merchant account, obtain API keys, and then manually link the payment gateway to your checkout portal. With an integrated ecosystem like Shopify, all this is already taken care of.

Intuit is also investing heavily in integrated payment technology. QuickBooks, the company’s signature accounting software solution for SMEs, isn’t just a platform for recording, categorizing, and reconciling transactions. Today, QuickBooks is also an integrated payment processing service that lets you accept payments in-store and online. Once payments are captured, and transactions are automatically recorded and categorized in the QuickBooks accounting system; no manual bookkeeping required. 

Key Features to Look For With Integrated Payments

Not all integrated payment systems will pair seamlessly with every one of your existing information systems. But, they should all meet certain basic criteria:

PCI Compliance

PCI Compliance

All payment providers should adhere closely to the Payment Card Industry Data Security Standard (PCI-DSS). Remember: compliance is a must. Adhering to industry regulations can help you protect your customers’ sensitive card information, steer clear of fines, and avoid being blacklisted.

Tokenization & Encryption

Tokenization & Encryption

Sensitive information is most vulnerable when it’s in transit. An integrated payment system that supports tokenization, and which offers some additional encryption solution for payment card information, can make that data less prone to compromise by bad actors.

Recurring Billing & Subscription Support

Recurring Billing & Subscription Support

A robust integrated payment system should support both one-time and recurring purchases. Transaction data needs to be synced to other information systems carefully so that it is processed correctly, though. For example, proceeds from an annual subscription plan, if paid upfront, must be recognized as revenue over time, rather than all at once.

Reporting & Analytics

Reporting & Analytics

An integrated payment system is powerful because it shares transaction data seamlessly with your other information systems. For this reason, a full-featured reporting and analytics system that spans all of your platforms is a must-have. This single source of truth can enable you to draw unique and compelling insights that you could’ve otherwise missed.

Multi-Channel Support

Multi-Channel Support

Like all payment processors, an integrated payment system should not be rigid. Instead, it should support a diversity of payment methods and checkout arrangements, whether online, over the phone, or in-person. This heightened flexibility makes it more likely that your buyers will be able to pay with their preferred payment method.

Increased security for transactions is important

...but it won’t protect you from all types of payment fraud.

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Challenges & Considerations With Integrated Payments

Integrated payments sound excellent in theory. You get to cut down on manual data wrangling, and all your information systems work together in the background. But, there are some downsides to consider:

Technical Integration Complexity

Technical Integration Complexity

A fully-integrated payment system is more sophisticated than a standalone payment processing solution. The process of integrating a payment system itself may take many hours of development time, plus deep knowledge of other components of your tech stack. There will also be ongoing troubleshooting requirements even after initial setup.

In any case, it’s not a walk in the park. You should expect integration to take a substantial upfront investment of time and money.

Vendor Lock-In Concerns

Vendor Lock-In Concerns

You don’t have to integrate a payment system from the ground-up. You can also choose out-of-the-box solutions (e.g. Shopify Payments or QuickBooks Payments) that come pre-integrated with one or more information systems. The difficulty, however, is that you may have a hard time switching away from a vendor if their solutions become so deeply embedded into your operations.

Besides, prepackaged integrated payment systems often feature tighter integrations with certain components of your tech stack and weaker integrations with others. For example, Shopify Payments is most closely linked with Shopify’s eCommerce platform, while QuickBooks Payments is most tightly integrated with the QuickBooks accounting platform.

Data Migration Risks

Data Migration Risks

Chances are, you already have an existing payment processing provider. If you’re looking to switch to an integrated payment system, you’ll need to port over your existing data into your new solution.

This is no trivial task. Data can easily become lost or corrupted during migration, which means you risk losing critical transaction information in the process. Out of an abundance of caution, create a backup of your data before you attempt to migrate anything over.

Costs & Fees

Costs & Fees

An integrated payment system can be more expensive than a standalone service. That’s natural; an integrated solution is more functional and desirable than a standalone module, and you may find the additional expense to be worth it.

The key here is to find an integrated solution that produces a positive return on investment. Does the time and labor saved exceed the incremental cost of your integrated payment system? If so, go for it. Just make sure that pricing is laid out fairly and transparently so that you can accurately estimate ROI.

Finding the Right Integrated Payment Processing Partner

An integrated payment platform obviously has a lot to offer. So, how do you get started?

Not every payment processing provider can help you integrate your operation. Your first step is to locate the best processing partner for your business. Here are a few things to consider as part of your search:

Think Like a Customer

Beyond what you’ll require from a processing partner, it’s good to also think about your customer’s needs. A range of payment options, for example, along with a secure, frictionless, and uniform purchasing process across all channels, can be very desirable.

Remember What You Came For

When shopping for a processor to help you integrate, don’t just look at features or cost. You’re not after a product; you’re looking for a solution. Have a clear idea of your requirements before you approach potential partners.

Make Security a Priority

Digital payment security is critical for eCommerce businesses. Be sure your integrated processing partner follows “best practices” for data storage and maintains PCI compliance to safeguard sensitive customers' information.

Will They Grow with You?

If you’re hoping to see your business grow, you’ll want your integrated payments system to be able to scale with your company as it expands. Look for providers that have the resources and stability to process an increasing volume of payments.

Be Sure They’ve Got Your Back

What kind of customer support will you need? Check reviews and, if possible, talk to existing clients. Providers who have a reputation for quality customer service and support aren’t likely to disappear once the contract is signed.

Does your business need integrated payments? The short answer is “yes.”

Think about the kind of shopping experience you want to offer your customers: fast, easy, and secure. Now, think about the sales experience you want for your operations: streamlined, accurate, and as easy as possible.

Integrated payments can help you accomplish both of these things.

That said, the exact structure of an integrated system is unique to every business. To reap the full advantages of integration, you’ll need to look at all your requirements, from payment options to security and fraud protection. At Chargebacks911, we’re familiar with all the components needed for secure processing. If you’d like help finding your best solution, contact us today.

FAQs

What is an example of an integrated payment?

One example of an integrated payment is an online checkout flow that’s to the merchant’s QuickBooks account. Upon payment, the transaction is automatically entered and categorized within the merchant’s QuickBooks accounting software.

What are the benefits of integrated payments?

Integrated payment solutions save time normally needed for entering and reconciling payments, which reduces your costs and streamlines cash flow. They also lower the potential for errors by eliminating manual data entry. Most importantly, they greatly increase the security of data storage and transmission.

How do you integrate payment services?

Talk to your gateway provider or processor. If they handle integrated payments, they can help you set it up.

What is the difference between integrated and non-integrated payment processing?

Integrated processing is built into the point-of-sale or customer relationship management (CRM) software being used. It does not typically require re-entry of the transaction amount, but rather pulls the amount from the software itself.

Non-integrated processing typically requires a human to manually input the amounts, often in more than one location. This takes time and opens the possibility of errors in recordkeeping and data transmission.

What does payment integration mean?

Payment integration occurs when a merchant’s payment processing system is linked to their customer relationship management (CRM) software, accounting software, order management system, and website. This creates a seamless ecosystem that is secure, but allows for data to be pulled and shared across multiple platforms.

What is an integrated payment system?

An integrated payment system is a payment processing system that is tightly linked to other information systems, including a merchant’s website, order management system, accounting system, and customer relationship management (CRM) system.

What is the difference between integrated and embedded payments?

Integrated payments involves connecting different information systems together, while embedded payments refer to payment processing capabilities that are built into a single system.

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