Stripe vs PayPal: Better Alternatives for B2B ERP Users

The payment solutions you choose aren’t just operational decisions—they’re strategic ones.

For growing businesses, especially in the B2B space, the wrong processor can quietly drain profit, hinder scalability, and complicate your tech stack.

And yet for many, the choice still comes down to Stripe vs PayPal—because those are the names everyone knows.

When Jake launched his food distribution business, he didn’t spend weeks researching payment transaction processing. He picked the names he recognized—Stripe and PayPal felt like the only real options.

Set up was easy, payments rolled in, and all seemed well—until his B2B business started to rapidly grow with large orders.

That’s when things got complicated.

Between flat-rate fees, held funds, deduction of credit card fees with every daily deposit, and an ERP integration that was designed to be a general solution for many ERP software platforms (not specifically the one Jake was using), Jake realized that what works for a retail consumer business doesn’t easily scale for serious B2B business operations.

For B2B companies processing high-value transactions, choosing the right payment solution isn’t about brand recognition—it’s about minimizing long-term costs, white glove customer support, and technology fit.

Stripe vs PayPal - The Allure of Both

There’s a reason these two names dominate checkout pages. Stripe’s developer-first reputation and PayPal’s widespread consumer trust make them easy wins for startups and small consumer businesses.

Their APIs are slick, onboarding is simple, and they support global transactions straight out of the box.

For new business owners, the decision often feels like Payment Processing 101—just pick a provider that works and move on.

But for B2B operations? It’s a different story.

When your revenue depends on ERP integration, invoice-level accuracy, and transaction volume optimization, PayPal vs Stripe becomes less about convenience and more about compromise.

These platforms weren’t designed with Dynamics 365 Business Central users or complex B2B workflows in mind.

What You Don’t See on the Pricing Page

Flat-Rate Fees vs Interchange Optimization

Payment processors like Stripe and PayPal advertise flat-rate pricing because it’s predictable. But predictability isn’t the same as profitability.

Many businesses overpay by 20–30% compared to what they’d spend using interchange-optimized rates, especially when Level 2 and Level 3 data processing is an option.

That’s not a rounding error... it’s a missed opportunity.

According to Forbes, more B2B companies are abandoning one-size-fits-all payment platforms in favor of providers that tailor rates to transaction details, card types, and buyer profiles​.

But even with cost optimization in place, things can go sideways fast without the right support.

When transactions fail, funds get held, or errors hit your ERP sync, who you can call—and how fast they respond—makes a world of difference.

Support That’s Not Built for You

High-stakes transactions need high-touch support. But try calling Stripe or PayPal when you have a question about a failed credit card or ACH transaction or a missing settlement, and you’re routed to a chatbot or a general support queue.

For businesses moving millions through their systems, that’s beyond frustrating. It’s risky.

Modern payment processing solutions for B2B enterprises should include a dedicated relationship manager; someone who understands your transaction flows, ERP setup, and business structure.

That level of support can prevent downtime, resolve issues faster, and help you achieve better financial results.

ERP and eCommerce Integration Challenges

Stripe and PayPal can connect to a lot of things, but integrating into Dynamics 365 Business Central in a way that fits your specialized business process isn’t what they are focused on doing for you.

Integrations are possible but often require custom development or third-party middleware, which adds costs, reduces reliability, and slows down issue resolution.

Tools like card account updater or line-item Level 3 automation aren’t easily available either, resulting in friction for customers and triggering higher Visa/Mastercard fees.

For businesses that rely on automation, data accuracy, and financial transparency, integration issues are a real dealbreaker.

There’s a Better Way: Tailored Credit Payment Processing

Before choosing a provider, it’s important to define “What is a payment platform” and what it should actually do for a B2B organization—especially when ERP integration is critical.

Before locking in a payment provider, here are some questions to ask:

• Can this solution scale with our transaction complexity and growth plans?

• Is it seamlessly embedded within Dynamics 365 Business Central and our eCommerce platforms?

• Does our payment provider specialize in Business Central or are they a generalist working across dozens of ERP platforms?

• Does it provide rock-solid security with PCI compliance from end-to-end?

• Are we optimizing fees—or just accepting what’s easy?

• Do we have support from someone who knows our business, or a ticketing system and a 1-800 customer support center?

These questions aren’t picky—they’re strategic. Composable, API-driven payment platforms are quickly replacing legacy or consumer-first tools because they deliver flexibility, integration, and cost efficiency.

A recent Forbes Business Council piece explains how this shift is helping B2B companies break free from the limitations of traditional gateways.

The right provider optimizes not only cost, but efficiency, scalability, security, and business continuity.

Why USTPay is Built for B2B

A recent Accenture Report notes that B2B businesses are moving beyond disruptors like Stripe in favor of solutions that prioritize integration, strategy, and support.

USTPay specializes in payment solutions designed for Dynamics 365 Business Central users, specifically B2B businesses with complex needs.

Here’s what that looks like in practice:

ERP Integration: Native support for credit card and ACH payments inside Business Central—no workarounds required.

Level 3 Data: Automate line-item capture to reduce interchange fees and improve reporting accuracy.

Multiple Gateways: Choose from 120+ PCI-compliant gateways and run multiple processors simultaneously to support multi-entity structures or failover protection.

Freedom of Choice: As a Business Central ERP user you also have the flexibility to bring-your-own-processor (BYOP), which means you don’t need to change your processor if you find that you are working with a B2B specialist that is meeting your needs.

Global Reach: Process international payments in multiple currencies without tacking on custom dev work.

Premium Service: Work with a dedicated relationship manager—no 1-800 numbers, no generic support tickets.

Final Takeaway: Convenience Costs More Than You Think

Stripe vs PayPal might be the default options, but default isn’t always better.

For B2B organizations with real payment complexity, these platforms are often more expensive, less scalable, and harder to support than alternatives designed specifically for your ERP and business model.

At USTPay, we help clients cut the costs of processing payments by up to 30% while improving transaction visibility, data accuracy, and ERP efficiency. If you’re still relying on flat-rate processors and patchwork integrations, maybe it’s time to rethink your strategy.

Schedule a consultation to uncover hidden savings and build a smarter, scalable payment solution that supports your business growth.

About Wade Tetsuka:

Wade Tetsuka is a visionary leader with over 15 years of experience as President of U.S. Transactions Corporation, where he has helped transform the landscape of B2B merchant services.

His deep expertise in finance, coupled with a keen understanding of compliance and client management, has positioned UST–a leading Fintech company and Independent Software Vendor (ISV) for Microsoft Dynamics 365–as a trailblazer in helping businesses save money and streamline payment processes.

As the founder of Presidential Forum LLC, an exclusive network for C-level executives, Wade fosters thought-provoking discussions that shape industry trends and leadership strategies. His commitment to excellence and forward-thinking approach makes him a sought-after voice in both the Fintech and executive leadership arenas.

Connect with Wade on LinkedIn.