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B2B Payment Gateway: Pros and Cons of Each Way Businesses Pay

A B2B payment gateway takes card and ACH payments against invoices and posts them to your ERP. This guide covers the pros and cons of each way businesses pay, from credit cards and ACH to wires, checks and direct debit, and what a gateway has to do for B2B.

Updated November 3, 2026

For the buying side of this, see B2B payment processing with Clarity Payment Hub: consolidated, partial and credit-applied payments that post to your ERP.

What Are B2B Payments?

Digital B2B payment solutions make it easier to send, receive, track, and record B2B payments. This is beneficial for both the buyer and seller in terms of accuracy, speed, and efficiency.

Electronic records enable businesses to have a more complete view of their financial activities. It also helps businesses identify any payment gaps or irregularities with ease. These types of B2B payment solutions can enable the entire payment process between the parties involved, reducing manual processing time and enabling real-time transaction status updates.

The 6 Most Common Types of B2B Payments

How B2B Payments Are Most Commonly Made

Let's take a closer look at these B2B payment methods and how each works.

A payment gateway can streamline payment processes for accounts receivable.

Credit Card Payments: Pros and Cons

Credit cards have become one of the most common and convenient ways for businesses to conduct transactions and manage financial obligations. Credit cards offer a variety of benefits that make them attractive for businesses and consumers alike.

ACH Payments (Automated Clearing House) Payments: Pros and Cons

ACH payments have become an increasingly popular form of digital payment for businesses in recent years. Unlike traditional methods of sending paper payments, ACH transactions are processed electronically and can be used to transfer funds from one entity to another using a routing number or a bank account.

Bank Transfers/Wire Transfers: Pros and Cons

Wire transfers are a popular and convenient payment method for businesses to send and receive secure payments. As an electronic form of payment, this form of payment offers real-time transactions with quick access to funds.

Checks or E-Checks: Pros and Cons

Despite the significant decrease in recent years, many companies are still using checks to make B2B payments due to the need for additional security measures and data exchange.

Paper Checks

E-Checks

An e-check is an electronic version of a traditional paper check. It is used to make payments online, typically via an automated clearing house (ACH transaction). Instead of writing out a paper check and sending it through the mail, the user provides their bank account information, which is then electronically sent to the recipient's bank.

Direct Debit: Pros and Cons

Much like an e-check, direct debit involves funds being removed from a checking account. Direct debit is a payment method where funds are directly withdrawn from a payer's account and transferred to the recipient's account.

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Top Reasons Companies Use B2B Payment Gateway Software

Businesses use B2B payment gateway software for a variety of reasons, primarily for the added security it provides when transferring funds online. It also allows for improved scalability, providing businesses with more opportunities to expand, as well as allowing them to simplify their accounting and financial operations.

B2B payment helping a company manage cash flow.

Better Cash Flow

Businesses should always consider how easy it is for customers to pay them. Payment portals are available that allow merchants to securely accept payments online via credit card or ACH/bank transfer without having to wait for checks or other paper transactions to arrive in the mail.

These solutions save time and make it easier to track payments, maximize profits, and improve customer experience by providing a smooth payment process.

Simpler Accounting

A complete B2B payment solution is an effective way to simplify accounts payable and accounts receivable, eliminating manual labor and reducing the risk of errors. By implementing this software with B2B payment features, check payments can be scanned, recorded, and stored automatically with no need for human intervention.

In addition to delivering convenience and accuracy, this type of payment solution can also integrate with popular enterprise resource planning (ERP), accounting, or bookkeeping programs.

A B2B payment system also helps businesses manage their finances more effectively by providing visibility into cash flow and tracking where money is coming in and out of the organization.

Save Time

Adopting B2B payment solutions is a great way to save resources such as time, money, and effort for businesses and customers alike. Instead of having to write and deliver checks manually, merchants can now use digital systems which automate the entire process.

In addition to saving time and money, B2B payment hubs also help simplify tracking payments from customers as well as keep an accurate record of all transactions made. This allows for better transparency in business operations along with more efficient reconciliation processes which reduce the need for manual labor that would otherwise take too much time and energy.

The Challenges of Digital Payment Options

B2B payment methods continue to evolve, as some become more common while others are slowly phased out. But with the introduction and expansion of these payment methods, problems obviously arise.

Let's talk about some of the challenges you'll need to address as you investigate electronic payment platforms, specifically with the digital version of these payments.

Security

Digital payments involve the exchange of sensitive financial data, and thus must be secured to protect against cyber-attacks and fraudulent activities. Encryption, tokenization and two-factor authentication should be used to ensure that customer data remains secure.

Compliance

Governments and other organizations regularly update their rules and regulations regarding digital payments, requiring businesses to keep up with the changing landscape in order to remain compliant. Failure to do so can result in costly fines and penalties for non-compliance.

User Interface

The user experience of payment portals should be simple and straightforward in order to maximize adoption by customers. If you don't, they are likely to switch to competing services that offer a better experience.

Costs

Implementing digital payment systems requires an investment of capital, including costs associated with technology, infrastructure upgrades, security measures, personnel training, and more. All of these add up quickly for businesses on a tight budget, so it's important to find a payment portal that isn't expensive in the first place and offers ways to avoid fees associated with electronic funds transfers.

Integration

When switching from one digital payment system to another (e.g., from cash registers to eCommerce), businesses need smooth integration between existing databases and software processes in order for the transition to occur without disruption. This process may require technical expertise or help from software engineers in order to integrate the new system into the existing architecture properly.

Fees

One of the biggest downsides of accepting digital payments is associated fees, which can cut into businesses' profits if not managed properly. Transaction fees, processing fees, and merchant services fees can all add up quickly, eroding any potential profits that may have otherwise been achieved through digital payments.

What a B2B payment gateway needs to do

A consumer checkout takes one card payment for one order. A B2B payment gateway has to take payments against invoices, by card and by bank, and get each one onto the right invoice in your ERP. Here is what to look for, and how Clarity Payment Hub handles each one.

Paying on account in Clarity Payment Hub
Paying on account in Clarity Payment Hub.

Payment Hub connects to NetSuite, Sage Intacct, Acumatica, Business Central, Epicor Kinetic, SYSPRO and more; see ERP payment processing.

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FAQ

What is the difference between a B2B payment gateway and a payment processor?

The gateway carries the payment details from your portal, website or ERP to the processor and returns the result. The processor moves the transaction through the card networks or the ACH network to the banks. Many companies sell both together, but they are separate jobs.

What is a B2B payment platform and who uses them?

A B2B payment platform is a digital system used to enable business-to-business payments. This payment processing enables companies to securely make and receive payments via multiple digital payment methods, with funds moving directly between two bank accounts from business to business.

B2B payment processing typically includes features such as B2B payment processing, transaction tracking, invoice automation, accounts receivable processing, international payments processing, recurring payments, and secure data sharing, allowing businesses to simplify their payment processes.

How do B2B payments differ from B2C payments?

B2B payments differ from B2C payments in a few key ways. B2B payments typically involve larger sums of money, as businesses are often making large purchases and may need to spread out the cost over time. Also, B2B payments involve more complex processes with additional layers of security and compliance checks.

Businesses also usually have more stringent payment terms compared to consumer transactions. Because of their complexity, B2B payments require support from specialized technology solutions such as enterprise-grade payment gateways or automated clearing houses that enable smooth transactions between parties.

Are B2B payment gateways compliant with data protection laws?

Reputable B2B payment gateways adhere to data protection laws, such as the General Data Protection Regulation (GDPR), and to the Payment Card Industry Data Security Standard (PCI DSS), the card industry's security standard. It is essential for businesses to choose B2B payment processing that complies with these requirements to safeguard customer data and avoid legal issues.

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Stephen Beer

Stephen Beer

Stephen Beer is a Content Writer at Clarity Ventures and has written about various tech industries for nearly a decade. He is determined to demystify HIPAA, integration, and eCommerce with easy-to-read, easy-to-understand articles to help businesses make the best decisions.

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