How Payment Processor Selection Impacts Microsoft Dynamics 365 Projects
You’ve signed the SOW. Timelines are set. Your team is excited about go-live. Then someone asks: “What about payment processing?”
If the answer is “We’ll figure that out later” or “Just use what we’ve always used,” your D365 implementation just became significantly riskier.
Payment processing isn’t a footnote in ERP projects—it’s infrastructure that touches every transaction, every customer interaction, and every financial close. When it goes wrong, it doesn’t just slow things down. It stops them completely.
Here’s why payment processing is the risk most Microsoft Dynamics partners hope to avoid—and what it costs when they do.
The Line Item Nobody Wants to Own
Ask any solution architect what they think about payment processing, and you’ll get the same response: high risk, low margin, always complicated.
Partners know payment selection can derail timelines. They know every client has different requirements. They know CFOs have strong opinions about processors and contracts. So what do they do?
They punt.
“Payment processing: TBD.”
“We’ll use whatever processor you’re currently using.”
“Microsoft recommends Adyen—let’s just go with that.”
The problem? None of these approaches actually address whether the solution fits your business. They’re strategies for avoiding the conversation, not solving the problem.
When “TBD” Becomes a Crisis
Here’s what happens when payment processing gets deprioritized:
Timeline Delays
Payment testing happens last. Integration issues surface two weeks before go-live. Suddenly, you’re scrambling to fix connector problems, API mismatches, or missing features that nobody mentioned during vendor demos.
Real example: A national retailer implementing D365 Commerce discovered critical marketing features—customer phone number lookup, email capture, loyalty program integration—weren’t actually included in their first-party payment solution. This revelation came during UAT, just weeks before a 280-store rollout had to start.
The fix? Long nights, offshore developers, and a solution literally sketched on the back of a kids’ placemat at a brewery.
CFO Pushback
Solution architects don’t choose payment processors. CFOs do.
A partner can spend months crafting the perfect SOW, only to have the finance team reject the payment recommendation entirely. “You think you get to decide who processes our transactions? Pound sand.”
This isn’t theoretical. It happens on nearly every enterprise deal. Partners who assume they’ll dictate processor choice discover—often late in the sales cycle—that they have zero authority over that decision.
Scope Creep Nobody Saw Coming
Payment processing requirements are deceptively complex:
- Card present vs. card not present (different rates, different hardware)
- PCI compliance and P2PE validation
- Multi-currency and cross-border transactions
- ACH, wire transfers, payment plans
- Fraud protection and chargeback management
- Integration with existing banking relationships
Each of these can add weeks to timelines and thousands to budgets if not planned upfront. But most SOWs treat payments as a single line item, not a multi-faceted integration challenge.
The Technical Risks Partners Underestimate
Even when payment processing makes it into project planning, technical assumptions can sink implementations:
The Connector Mismatch
Not all payment connectors support all D365 modules equally. A connector that works beautifully for F&O back-office transactions might have zero support for Commerce omnichannel scenarios. Partners discover this when it’s too late to change direction.
The “First-Party” Trap
Microsoft’s first-party payment solution sounds perfect: seamless integration, vendor support, no third-party risk. Until you realize the D365 integration uses legacy APIs, not the modern features the payment vendor is actively marketing.
What the vendor promises in their sales deck and what’s actually available in the Microsoft integration are often two very different things.
The Hardware Lock-In
Choose the wrong processor and you’re locked into their proprietary terminals. Want to switch in three years? You’ll need to replace every device across every location. For a retailer with 200+ stores, that’s not just inconvenient—it’s a six-figure mistake.
The Financial Impact of Getting It Wrong
Payment processing mistakes aren’t just technical headaches. They cost real money:
Delayed Go-Live: Every week your implementation slips costs your organization in lost efficiency, extended consulting fees, and delayed ROI. Payment issues are one of the top reasons D365 projects miss deadlines.
Unfavorable Contract Terms: Sign without negotiation and you’ll pay:
- Higher interchange rates (that 0.2% difference costs millions annually for high-volume businesses)
- Expensive device leases or buyouts
- Locked-in contracts with auto-renewal traps
- Hidden fees for features you assumed were included
Rework Costs: Switching processors mid-implementation or post-go-live means rebuilding integrations, reconfiguring workflows, and retraining users. Budget at least 80-120 hours of developer time—and that’s if everything goes smoothly.
Why This Risk Exists (And Persists)
If payment processing is such a critical risk, why do partners keep treating it as an afterthought?
It’s not their expertise. Solution architects are ERP experts, not payment industry experts. They know Dynamics modules inside and out. They don’t know which processors excel at B2B ACH vs. retail card-present transactions.
It’s low margin. Partners make money on implementation services, customizations, and ongoing support—not payment consulting. Spending time on processor selection doesn’t improve their bottom line.
It’s high risk. If payment integration fails, the blame falls on the implementation partner. Why take on that exposure for minimal financial upside?
The result? Partners either avoid the topic entirely or default to the easiest answer (Microsoft’s first-party solution), regardless of whether it actually fits the client’s needs.
The Solution: Plan Payments Early, Choose Strategically
Payment processing doesn’t have to be a crisis waiting to happen. Organizations that treat it as a strategic decision—not a procurement checkbox—consistently deliver smoother implementations and better long-term outcomes.
Start Early: Address payment strategy during pre-sales or project kickoff, not during UAT. Map your actual payment flows (card present, card not present, ACH, international) and translate those into technical requirements.
Evaluate Objectively: Don’t default to “what we’ve always used” or “whatever Microsoft recommends.” Evaluate 3-5 options based on your specific architecture, transaction patterns, and business model.
Negotiate Strategically: ERP migrations create leverage. Processors will compete for your business if they know alternatives are on the table. Use that leverage to secure better rates, free hardware, or implementation subsidies.
Get Expert Help: Partner solution architects are brilliant at ERP implementation. They’re not payment processing negotiators. Bring in a specialist who knows both worlds—someone who can bridge the gap between Dynamics architecture and payment industry dynamics.
Protect Your D365 Investment
Payment processing is infrastructure, not an IT checkbox. Treat it like infrastructure—plan it early, choose it strategically, and ensure it aligns with both your technical requirements and your business goals.
The alternative? Hoping nothing breaks two weeks before go-live.