B2B Payments: Best Practices to Secure Payment Processing

Your finance team just approved a $50,000 payment to a supplier. The wire transfer goes through smoothly. Monday morning, your supplier calls asking where their payment is. Your bank confirms the money left your account, but it went to fraudsters who intercepted the payment details through a business email compromise attack. The money is gone, and you're now facing angry suppliers, compliance investigations, and a board that wants answers.

If you're processing B2B payments, you're dealing with risks that dwarf typical consumer financial transactions. While the story above highlights wire fraud, attackers target every payment rail available, from corporate credit cards to virtual accounts. Unlike a $50 purchase at an online store, B2B payments involve large sums that make them attractive targets for sophisticated fraud.

Recent data from the 2025 AFP Payments Fraud and Control Survey shows that 79% of organizations were targets of payment fraud in 2024. Add multiple approval chains, various stakeholders, complex payment methods, and strict compliance requirements, and you have a payment ecosystem where a single payment security gap can cost you more than your annual revenue.

In this guide, you'll learn how to build secure B2B payment systems that protect your transactions from fraud while meeting compliance standards. By the end, you'll know:

• How to authenticate high-risk card payments using 3D Secure 2 to shift fraud liability
• When and how to implement tokenization to protect payment information in recurring B2B payments
• How virtual accounts simplify reconciliation while providing a secure payment method
• Methods to monitor suspicious activity in real-time before money leaves your account
• Data protection practices that keep sensitive information secure throughout the payment flow

Why B2B Payments Need Extra Security

The attack surface and potential impact of a B2B payment failure are much larger than failures in the consumer space. Here is what makes the risks so much higher.

Transaction size matters: When you're processing $100,000 invoices instead of $100 purchases, fraud becomes more lucrative. Attackers know this and specifically target B2B payment flows. They gravitate toward legacy fraud methods where large sums are most vulnerable. This is why check fraud remains the top source of B2B payment losses, because a single compromised check can drain significant funds before anyone notices.

Multiple stakeholders create more attack vectors: A typical B2B payment might involve your procurement team, finance department, the vendor's sales team, their accounting department, and various approval workflows. Each person and system in that chain is a potential entry point for attackers. Business email compromise (BEC) attacks exploit exactly this complexity by impersonating executives or vendors to redirect payments.

The data risk: The data being exchanged is not just a credit card number. It includes sensitive business information, financial records, and vendor/client lists. A breach can lead to devastating, cascading consequences: immediate financial loss, severe regulatory fines for non-compliance with standards like PCI DSS or data-privacy laws, and a permanent loss of trust that can destroy a business's reputation.

The stakes are clear: large transactions make you a target, multiple stakeholders create more entry points for attackers, and the sensitive data flowing through your systems demands protection at every step.

Best Practices for Secure B2B Payment Processing

There is no single "silver bullet" for secure payment processing. A resilient B2B payment architecture is built on a layered security model, where each principle and practice is designed to defend against a specific attack vector. As an engineering lead or developer, your role is to architect these layers, building a system that is secure by default.

1. Authenticate High-Risk Credit Card Payments with 3D Secure 2
3D Secure 2 (3DS2) adds a critical authentication layer for credit card payments by verifying that the person making the online transaction actually owns the card. It's one of the most effective authentication methods for online payment security.

Here's how it works: when processing a payment, 3DS2 transmits over 100 data points to the cardholder's bank, including device ID, transaction history, and shipping address. The bank uses this information to assess risk, triggering one of two flows:

• Frictionless Flow: For low-risk transactions, the payment proceeds immediately without any user interaction.
• Challenge Flow: For higher-risk payments, the cardholder must authenticate using their banking app, biometrics (fingerprint or facial recognition), or an OTP.

How Flutterwave Can Help
Flutterwave supports 3DS2 automatically through payment APIs and Checkout. When you initiate a card charge, Flutterwave detects if 3DS2 is required and handles the authentication flow. If the card requires 3DS authentication, the response includes a redirect URL where customers complete verification with their bank.

The security features here are substantial: 3DS2 shifts chargeback liability for fraudulent transactions (like stolen credit card usage) from you to the cardholder's bank. If someone uses a stolen card and passes 3DS2 authentication, the financial institution bears the loss, not your business. This makes 3DS2 a core part of any payment security strategy.

2. Prevent Data Breaches with Payment Tokenization

Storing card details for recurring B2B payments is both a security risk and a compliance headache. Tokenization solves both problems.

Instead of storing actual card numbers, tokenization replaces them with unique tokens that represent the customer's payment method. Even if intercepted, these tokens are worthless to attackers because they cannot be reverse-engineered into card details or used to transact on any other platform.

How Flutterwave Can Help
Here is the step-by-step developer flow for securely implementing recurring B2B payments using Flutterwave's tokenization:

Step 1: The Initial Charge: First, you must charge the customer one time to create the token. This is typically done using a secure, hosted solution. We recommend Flutterwave Inline, which isolates your systems from the card data.

Step 2: Verify and Extract Token: After the customer completes the initial payment, your backend must call Flutterwave's verify endpoint for that transaction. In the successful JSON response, you will find the token field nested within the data.card object.

A sample verification response might include:

{
  "status": "success",
  "message": "Transaction fetched successfully",
  "data": {
    "id": 285959875,
    "tx_ref": "YOUR_TX_REF",
    "status": "successful",
    "amount": 5000,
    "currency": "USD",
    "customer": {
      "email": "[e-mail]"
    },
    "card": {
      "first_6digits": "553088",
      "last_4digits": "2950",
      "issuer": "MASTERCARD",
      "type": "MASTERCARD",
      "token": "flw-t1nf-93da56b24f8ee332304cd2eea40a1fc4-m03k"
    }
  }
}

Step 3: Store the Token: In your backend database, you will now save this token: flw-t1nf-93da56b24f8ee332304cd2eea40a1fc4-m03k. Link this token to the customer's profile using their unique user ID and the email address used for the charge. You can also store the non-sensitive fields like last_4digits and issuer to display in your application's "Payment Methods" UI.

Step 4: Subsequent Charges. For all future recurring payments, your server will make a secure, server-to-server API call to the tokenized charge endpoint. You do not need the customer to be present. Here is the API endpoint:

POST https://api.flutterwave.com/v3/tokenized-charges

You will pass the required parameters in the request body, including the token you stored, the customer's email, the amount, and a unique tx_ref for this new transaction.

{
  "token": "flw-t1nf-93da56b24f8ee332304cd2eea40a1fc4-m03k",
  "email": "[e-mail]",
  "currency": "USD",
  "amount": 5000,
  "tx_ref": "recurring-sub-b2b-002",
  "country": "NG"
}

This API-driven flow ensures you can manage complex B2B billing cycles while architecturally eliminating the risk and compliance overhead of handling sensitive cardholder data.

3. Use Virtual Accounts for B2B Collections
Virtual accounts give each customer or transaction a unique bank account number for payments. This simple feature dramatically improves both security and reconciliation.

When you create a virtual account through Flutterwave, you get a real bank account number that routes payments to your business. Because each virtual account is unique, you instantly know which customer or invoice a payment relates to without manual matching.

How Flutterwave Can Help
Flutterwave offers two types:

1. Dynamic virtual accounts expire after one hour or first use. Perfect for one-time invoices where you need automatic reconciliation.
2. Static virtual accounts are permanent, tied to specific customers. Ideal for recurring B2B relationships where the same client makes regular payments.

# Create a static virtual account
curl --location 'https://api.flutterwave.com/v3/virtual-account-numbers' \
  --header 'Authorization: Bearer YOUR_SECRET_KEY' \
  --data-raw '{
    "email": "[email protected]",
    "is_permanent": true,
    "bvn": "1234567890",
    "tx_ref": "unique_reference"
  }'

The security advantage: virtual accounts eliminate payment redirection fraud. When customers pay directly to their assigned account number, there's no chance for attackers to intercept and change payment details. Plus, every payment triggers a webhook notification, giving you real-time visibility.

4. Combat Invoice Fraud with Integrated Payment Invoicing
The fundamental vulnerability of traditional B2B invoicing is the static, insecure PDF attachment. An attacker intercepts the email, uses a PDF editor to change the banking details on the invoice, and forwards it to the accounts payable department. The payment is then sent to the fraudster.

How Flutterwave Can Help
Flutterwave Invoicing provides an architectural solution that designs this fraud vector out of the process. Instead of attaching an insecure, editable file to an email, the Flutterwave system creates an end-to-end, secure loop.

How it works:

1. You create a professional invoice on your Flutterwave dashboard, detailing the services, cost, and due date.
2. Flutterwave sends an email to your customer containing a unique, secure link to view and pay this invoice.
3. When the customer clicks the "Pay Invoice" button, they are taken directly to a secure, Flutterwave-hosted payment page.
4. This page is already PCI DSS compliant and supports multiple payment methods (card, bank transfer, etc.), all secured by Flutterwave's infrastructure.

This system effectively short-circuits the most common and damaging B2B attack vector. It also provides significant operational benefits, such as automated payment tracking, status updates (e.g., "Paid," "Pending"), and automated reminders for overdue invoices.

5. Monitor and Alert on Suspicious Activity
Fraud prevention requires catching suspicious activity in real time, before the transaction completes. This means implementing fraud detection systems that monitor transactions, flag anomalies, and trigger alerts so your team can act before funds leave your account.

How Flutterwave Can Help
Flutterwave provides key monitoring layers:

• Transaction monitoring systems analyze payment patterns in real-time. Unusual transaction amounts, rapid successive payments, or payments from unexpected locations trigger automatic alerts.
• The 24/7 fraud desk is staffed with security specialists who review flagged transactions and coordinate with financial institutions when fraud is detected.

You should supplement Flutterwave's monitoring with your own application-level checks, like implementing velocity checks:

// Example velocity check using Redis
// We combine User ID and IP to avoid blocking legitimate corporate networks (NATs)
const attemptKey = `payment_attempts:${userId}:${ipAddress}`;
const attempts = await redis.incr(attemptKey);
await redis.expire(attemptKey, 3600); // 1 hour window

if (attempts > 10) {
  throw new Error("Too many payment attempts");
}

Best practice: Don't just log suspicious activity, act on it. Implement automatic blocks for clearly fraudulent patterns and manual review workflows for your finance ops team.

6. Protect Data Throughout the Payment Flow
Security means more than fraud prevention; it's about protecting sensitive customer data from the moment a payment is initiated to final processing.

How Flutterwave Can Help

• Encryption: Flutterwave uses advanced encryption protocols for all data transmission. When you send card details to the API, they're encrypted in transit using industry-standard TLS. Stored data is encrypted at rest.

• KYC and verification: Before merchants can process payments through Flutterwave, they undergo thorough Know Your Customer (KYC) verification. This prevents fraudsters from setting up fake merchant accounts. For customers, verification methods like BVN (Bank Verification Number) linking add another security layer.

• Access controls: Implement role-based access in your application. Not everyone on your finance or ops team needs permission to initiate payments. Your procurement team might create payment requests, but only finance should approve and execute them. Use multi-factor authentication for anyone with payment approval authority.

• Data minimization: Only collect and store the data you actually need. The less sensitive information you hold, the less you can lose in a breach. Use Flutterwave's tokenization to avoid storing card details entirely.

• IP whitelisting: Configure your Flutterwave dashboard to only accept specific server IP addresses for sensitive operations like payouts. Even if an attacker manages to steal your secret API keys, they cannot move funds because their requests will originate from an unauthorized IP and be blocked immediately.

Wrapping Up

Building secure B2B payment systems means thinking about security at every step. The best defense combines multiple layers: 3DS2 authentication to verify cardholders, tokenization to protect stored payment data, virtual accounts to prevent payment redirection, and real-time monitoring to catch fraud before funds leave your account. But none of these measures works in isolation; strong authentication won't help if poor access controls let unauthorized users initiate payments in the first place. Build security into every layer of your payment infrastructure.

Ready to implement these security practices? Create a Flutterwave account and start building payment systems that protect your business and your customers.