B2B payments: How they work + how to set up an efficient payment system

6 types of B2B payments

Like other transactions, businesses can make B2B or B2B2C payments in various ways. Here are six common business-to-business payment methods:

1. Checks 

While checks may be a less common form of payment for B2C transactions, they’re still fairly common for B2B transactions. Despite their frequent use, paper checks are one of the less convenient payment methods.

Accepting checks as a payment method can result in a less secure transaction. Checks are a major source of fraud because they lack the security measures of cards and electronic payments and can be easily faked or replicated. 

Still, the key benefit of checks is that they are often used as an alternative to avoid credit card processing fees. 

2. ACH payments

Automated Clearing House (ACH) transfer is an electronic payment option that transfers money directly from the payee’s financial institution to yours. ACH transfers can take up to three days to complete.

However, ACH payments are highly secure and typically completed at no additional fee to the buyer or seller. eChecks are a common type of ACH payment. 

3. Wire transfers

Wire transfers electronically move funds from a buyer to your bank account. This process is generally faster than an ACH transfer, allowing for real-time payments because businesses can transfer funds via a financial network. Wire transfers are typically completed within a few hours, taking up to one business day at the longest.

Remember that international bank transfers can take longer and incur higher payment processing fees, depending on the service provider.

Over the last few years, B2B payment solutions have grown significantly, thanks to innovations in payment processing and fintech, as well as the rise of e-commerce.

4. Digital payment platforms

Another popular B2B payment option is the use of digital payment platforms, such as:

• PayPal
• Google Pay
• Apple Pay
• Venmo

These digital payment platforms allow businesses to place a payment in real time, making it a more convenient option than other common small business payment methods, such as paper checks. 

You can make B2B payments using digital payment platforms via a website or mobile app. One downside to digital B2B payment services is that you’ll likely have to pay a transfer fee while sending or withdrawing a payment.

5. Credit and debit cards

Most companies have a business-only credit card, which makes it easier to track expenses on the billing statement. They’re an easy way to make payments both in person and digitally. 

Accepting all major credit cards—Visa, Mastercard, American Express, and Discover—will make buying your product easier at checkout and help you close more sales. Another great thing about credit card payments is that businesses tend to spend more when using them. Use our payment processing calculator to calculate rates and compare payment processors.

Clients may also use what’s known as a virtual card, which has a temporary credit card number and allows for safer online payments.

6. Cash 

Of course, this list wouldn’t be complete without including good old-fashioned cash. Unlike credit cards or other B2B payment options, those who use cash will never have to worry about paying any transaction fees or the risk of spending money they don’t have.

Because of this, cash is a popular option for businesses looking to minimize transaction fees. In some cases, a business may only accept cash. One downside of only using cash for B2B payments is that it can lead to a negative cash flow balance, as using cash immediately lessens your cash flow balance.

Challenges of B2B payments

Understanding the challenges associated with managing business payments can help you choose a payment system that works for your business and overcome these challenges. 

B2B payments are complex, particularly for midsize businesses, which don’t always have access to the right payment solution. B2B payment processing is often slow and inefficient –– leading to delays and cash flow management issues.

Here are a few common challenges that impact B2B payment processing:

• High processing costs: High processing costs lower your margins and take funds out of your revenue.
• Payment delays: Slow processing methods can lead to payment delays for both buyers and sellers.
• Time-consuming: Manually reconciling multiple invoices and processing data can be slow and inconvenient. Data is often missing, and it’s time-consuming for back-office teams to piece together data.
• Longer billing cycles: Most B2B payments allow for processing on a consistent cycle. Payment cycles can be as short as 30 days or even as long as 90 days.
• Tracking issues: Businesses will often manage more than one B2B transaction at a time. This creates challenges associated with processing, tracking, and reconciling many payments in different stages of the billing cycle.
• Low transaction visibility: Limited views of the transactions linked to multiple payment methods can disrupt the payment cycle, causing delays, extra costs, and chargebacks.
• Mismatched payment preferences: Limited views of the transactions linked to multiple payment methods can disrupt the payment cycle and cause delays, extra costs, and chargebacks.
• Risk of fraud: The risk of fraud is high due to minimal authorization controls for every transaction. B2B payments are often subject to security threats and fraud attempts. 

Benefits of B2B payment software

Many small businesses turn to B2B payment software to help combat these challenges. Read through the following benefits to learn more about the benefits of using B2B payment systems.

Flexible payment options 

As you know, there are many B2B payment methods. From digital payment platforms like PayPal, Venmo, and Apple Pay, to debit and credit cards, B2B payment software allows you to manage all of your payments in one place.

Automated bookkeeping

Another benefit of using a B2B payment platform is automated bookkeeping. As payments come in, the payment system works with accounting software, like QuickBooks, to automatically record each transaction, saving you time and minimizing the risk of human error.

Streamlined invoicing 

B2B payment software also allows you to create customizable invoices that your customers can easily pay online, allowing for a much quicker payment process than traditional paper invoicing.

In addition, you can also track your invoices to ensure no payments fall through the cracks. Not only will you be able to see when businesses pay your invoices, but you’ll also be able to see when they view them.

Quick and easy deposits

With B2B payment software, you can access your payments quickly and easily. You may even be able to access your payments instantly, eliminating the wait time that usually comes with paper checks or ACH transfers.

Recurring payment automation

If any of your B2B transactions are recurring payments, you can use B2B payment software to schedule recurring invoices automatically. B2B payment automation can also help save you and your employees time while reducing the risk of human error or a forgotten payment.

B2B payment trends in 2025

As technology advances, so does the B2B payments space. From a decline in paper checks to emerging payment methods such as digital payment platforms, let’s take a closer look at the B2B payment trends changing the landscape.

Payment automation 

Many businesses turn toward software that can help automate the B2B payment process and accept payments in real-time. From automatically sending invoices for recurring payments to keeping payment methods on file, payment automation can help speed up the B2B payment process.

Mobile payments and digital wallets

With mobile payment apps and digital wallets becoming commonplace for B2C transactions, they will likely be increasingly popular for B2B payments. This includes popular payment apps, such as Venmo and PayPal, as well as digital wallets, like Apple Pay and Samsung Pay.

To help your small business stay ahead of this trend, you may want to consider using payment software that accepts these popular forms of B2B payment.

Remote payment approvals

With remote work now being the new norm for some businesses, more and more B2B payments are being approved remotely rather than in a traditional office setting. Because of this, many businesses turn to electronic payments and invoicing to help simplify the payment process, regardless of your location.

Fewer paper checks 

With the speed and security benefits of alternative payment options such as credit cards and digital payment platforms, paper check usage has declined over the past few decades.

Because of this, small businesses must stay up to speed with other popular B2B payment options to ensure they are ready to accept other forms of payments as paper checks fall to the wayside.

How to set up a system for efficient B2B payments

Setting a proper system in place might seem like a big task, but modern tools make it much more manageable. Plus the payoff in efficiency and reliability is well worth it. You want a streamlined process that makes it easy for clients to pay you and easy for you to manage internally.

Key elements are ease of use and security. A secure payment gateway is crucial for building client trust when they pay online. While every business's needs differ slightly, here’s a more actionable approach to setting up your B2B payment system:

1. Choose the right payment solution provider

Don't just pick the first option. Evaluate providers based on your specific needs. 

Consider factors like:

• Transaction volume and size: The provider should be able to handle your typical payment amounts and frequency.
• Payment methods accepted: Ensure they support the methods your clients prefer and you want to offer (ACH, credit/debit cards, digital wallets like PayPal, Apple Pay, Google Pay). Look for options like QuickBooks Payments that integrate multiple methods.
• Integration capabilities: It needs to connect seamlessly with your existing accounting software to automate bookkeeping. 
• Fees and pricing structure: Understand the costs associated with different payment types.
• Security features: Look for robust fraud detection tools, encryption, and compliance certifications.
• Reporting and analytics: You should be able to easily track payment statuses, cash flow, and generate reports. 

Choosing thoughtfully upfront saves headaches later.

2. Integrate with your accounting system

Connect your chosen payment solution directly to your accounting software. This enables:

• Automated reconciliation: Automatically match payments received to open invoices, drastically reducing manual work and the associated time cost.
• Accurate record keeping: Minimize data entry errors by having payments automatically recorded.
• Improved cash flow visibility: Get a clearer, real-time picture of your finances within your accounting dashboard.
• Import existing client data to streamline setup.

Proper integration is the foundation of an automated payment process.

3. Configure accepted payment methods and terms

Once integrated, set up the specific payment options you want to offer clients within the system. Make it easy for them to pay online via ACH or card directly from an electronic invoice. 

Also, configure your standard payment terms within the system if it supports automated reminders or tracking based on due dates. 

Offering convenient options encourages prompt payment.

4. Establish clear internal workflows and training

Define how your team will use the system. This includes:

• Invoice creation and delivery: Standardize how invoices are generated and sent (preferably electronically with payment links).
• Payment approval process: If approvals are needed, define the steps, especially important for remote teams.
• Payment processing and reconciliation: Outline who handles receiving and applying payments within the system.
• Fraud prevention: Train your team not just on using the software, but also on security best practices – verifying large or unusual payment requests, recognizing phishing attempts, and understanding the system's fraud detection features.

Well-defined processes and trained staff minimize errors and risks.

5. Communicate with clients and go live

Inform your clients about your payment options, highlighting the convenience and security of electronic methods. Ensure your invoices clearly show how clients can pay online. 

Start sending invoices and processing payments through the new system. Monitor the process closely in the initial weeks to identify and resolve any issues quickly. A smooth rollout sets the stage for ongoing success.

Following these steps systematically can lead to a more robust and efficient payment workflow.

Choose the best payment setup for your business

With an understanding of B2B payments and the payment methods and trends shaping the payment process, you might consider using QuickBooks Money to process your B2B payments. While switching bank accounts may be time-consuming, QuickBooks Money offers payment tracking and a mobile business bank account you can use for B2B payments.

QuickBooks Payments: QuickBooks Payments account subject to eligibility criteria, credit, and application approval. Subscription to QuickBooks Online required. Money movement services are provided by Intuit Payments Inc., licensed as a Money Transmitter by the New York State Department of Financial Services. For more information about Intuit Payments' money transmission licenses, please visit https://www.intuit.com/legal/licenses/payment-licenses/.

Apple Pay: Apple Pay is a registered trademark of Apple Inc. 

Google Pay: Google Pay is a trademark of Google LLC.

QuickBooks and Intuit are a technology company, not a bank. Banking services provided by our partner, Green Dot Bank.

**Product Information:

QuickBooks Money: QuickBooks Money is a standalone Intuit product that includes QuickBooks Payments, and currently does not connect with other QuickBooks products such as QuickBooks Online (and QuickBooks Checking), QuickBooks Self-Employed, or GoPayment. Intuit accounts are subject to eligibility criteria, credit, and application approval. Banking services provided by and QuickBooks Visa Debit Card are issued by Green Dot Bank, Member FDIC, pursuant to a license from Visa U.S.A. Inc. Visa is a registered trademark of Visa International Service Association. QuickBooks Money Deposit Account Agreement applies. Banking services and debit card opening are subject to identity verification and approval by Green Dot Bank. Money movement services, including Same Day Deposit, are provided by Intuit Payments Inc., licensed as a Money Transmitter by the New York State Department of Financial Services.