Dynamics 365 payment gateway: a 10-question Business Central scorecard for MSPs

It's the last business day of the month. Your ConnectWise PSA says your biggest client paid on the 28th. Business Central still shows the invoice as open, and the deposit hasn't reached your bank. You can't close the month until those three line up, so you start digging.

A Dynamics 365 payment gateway won’t fix that on its own, even one built for Business Central. A payment gateway takes the payment. But a full payment integration finishes the job: it posts the payment to the right invoice in Business Central, records the deposit when the money actually lands, and keeps your PSA in agreement. If a payment fails, it tells you. For MSPs, accounting firms, and other service businesses running Microsoft Dynamics 365 Business Central alongside PSA tools like ConnectWise, that difference is what determines whether payments reconcile cleanly or turn into month-end delays, manual fixes, and weak cash flow visibility.

In this guide, we'll follow one client payment through a typical MSP stack and show where payment processing with Business Central usually breaks down. You'll see the checkpoints that matter, how to separate a gateway from a real Business Central payment integration, and how to use a 10-question scorecard to evaluate vendors, including how Alternative Payments supports these workflows, before you sign.

Is Microsoft Dynamics 365 a CRM or ERP, and which one do you run?

Microsoft Dynamics 365 is a family of apps. Some are customer relationship management (CRM) apps, like Dynamics 365 Sales and Dynamics 365 Customer Insights. Others are enterprise resource planning (ERP) apps, like Dynamics 365 Business Central and Dynamics 365 Finance, which run both accounting and operational functions. Each app handles payments differently, so a payment option built for one won't necessarily work in another. For more information on each app, check out this breakdown of Dynamics 365 products.

This guide focuses on Business Central, Microsoft's ERP for small and mid-sized organizations. More than 55,000 companies use it, and it's a common next step for MSPs that outgrow QuickBooks.

What Business Central's built-in payment tools cover (and where they stop)

Business Central includes two payment tools out of the box:

1. Payment Services adds a pay link to invoices you email so clients can pay online, which shortens the wait between sending an invoice and seeing cash. Today, PayPal is the main option, since Microsoft retired its WorldPay extension.
2. Payment Reconciliation Journal imports your bank statement, and Business Central suggests which open invoices each deposit belongs to based on the payment text. Someone on your team reviews the matches before posting.

Both tools work well when the payment carries its own details, but that’s not always the case. Chances are, your clients increasingly pay via Automated Clearing House (ACH) transfer. The Federal Reserve Bank of Cleveland found that ACH's share of business-to-business (B2B) payments rose from 25% in 2015 to 41% in 2024.

ACH deposits often arrive with a vague bank reference, while the invoice numbers show up later in a separate email. Another Federal Reserve Bank of Cleveland brief points to that split as the reason B2B matching stays manual and error-prone. For your finance team, that means toggling back and forth between the bank feed and the inbox to play detective. Automated reconciliation removes most of that manual bookkeeping, along with the errors that come with it. If you're working toward a back office that runs without you, a payment integration should take this work off your plate.

What happens when you follow one payment from creation to cash?

Picture a single monthly managed services invoice moving through your order-to-cash cycle. Between the day your PSA creates it and the day the cash clears, it passes through the following five checkpoints:

1. The invoice starts in your PSA

Your technicians log time and your agreements bill in PSA platforms like ConnectWise, Autotask, HaloPSA, or SuperOps.ai. Business Central holds the books. Before any payment moves, you need to decide which system owns the invoice and the client record.

If both systems can create or edit invoices, you'll eventually see duplicates, or edits in one system that never reach the other. A good payment integration syncs from one system of record and tells you plainly what happens to edits and deletions. If you're still shaping how your PSA and accounting tools work together, it helps to plan the PSA around finance first. Our ConnectWise and Autotask guides cover the trade-offs.

Ask your vendor: Which system creates and edits invoices and clients?

2. Your client enters card details or connects a bank account

Next, your client opens the invoice email and pays. Ideally, they can pay the open invoice right from the email or through a customer portal, by credit card, debit cards, or ACH. Some customers may also expect to buy online and then complete or manage payment through another commerce channel.

Bank payments raise one more question: how the client's account gets verified. Some platforms still rely on micro-deposits, which can stall client onboarding for days.

Ask your vendor: How do clients pay, and how do they connect a bank account?

3. Business Central records the payment

Once the client pays, Business Central needs to know. The payment transactions should post against the right open invoice, land in the account you expect, and handle partial payments without someone stepping in. Accountants call this cash receipt posting, and it’s a step worth automating for finance teams.

A vendor might promise "real-time updates," but you need to know whether that means minutes or hours, and which records move in which direction. Integrated payments also support customer experience by reducing delays, manual errors, and mismatched balances across systems. Your PSA needs the update too, or your account managers will see an open balance for a client who already paid. Here's how MSPs can keep their PSA reconciled.

Ask your vendor: What changes in Business Central when a client pays, how fast does it happen, and how does that status reach our PSA while managing payments inside Microsoft Dynamics 365?

4. The money reaches your bank

"Paid" in Business Central doesn't mean the money is in your bank. Three separate events need to happen: the invoice status changes, the payment platform sends a payout, and the deposit posts in Business Central.

For example, with Alternative Payments, standard payouts reach your bank 3 business days after a payment is processed. Build your cash flow forecast on the payout date, not the paid date.

Fees add another wrinkle. If processing fees come out of the payout before it lands, the deposit won't match the invoice total. A good integration records deposits to the bank account you choose and puts fees in a known account, so your payment processing costs show up where your controller expects them.

Ask your vendor: How are deposits and processing fees recorded in Business Central?

5. An ACH payment reverses

An ACH payment can bounce after the invoice already shows paid. Banks usually reject a bad payment within about 2 days, but a client can dispute an ACH debit for up to 60 days.

By then, Business Central and your PSA both show the invoice as settled. If the failure doesn't sync back, someone has to notice it, reopen the invoice, and fix the books, which adds operational and reconciliation risk. Reversals get more common as ACH volume grows. Nacha reported that B2B payments on the ACH Network rose 9.7% in Q3 2026, to nearly 2.3 billion.

Two healthy habits keep reversals from piling up: reconcile to payouts instead of invoice statuses, and review failed payments every week so payment operations are still being monitored when ACH reversals appear.

Ask your vendor: What happens when an ACH payment fails after the invoice shows paid, and who helps when a sync stalls?

Your 10-question Business Central payment integration scorecard

The walkthrough above surfaces most of what separates a payment integration from a gateway. Two more questions come before any payment moves: whether the product was built for Business Central, and how it connects. Together, they make a scorecard you can send to every vendor before a demo.

Grade each answer as documented, shown live, or "we'll get back to you." For broader criteria, see our questions to ask any billing platform. If a vendor slide deck promises "seamless integration," it doesn’t really answer any of these questions.

How Alternative Payments handles each checkpoint

Alternative Payments is, among many other things, a payment management solution that automates invoicing, payments, and reconciliation for MSPs across connected systems, and it integrates with the PSA and accounting tools you already run, such as ConnectWise, Autotask, HaloPSA, SuperOps.ai, and Business Central. Invoices and payments live in our Accounts Receivable platform, where you can send invoices and collect payment, and an extension called AccountLink connects it to Business Central. The Business Central guide walks through setup.

If you run a PSA alongside Business Central, you can connect both as dual integrations. One acts as your primary integration, the main source of truth for invoices and clients. The other acts as the secondary integration and receives payment status updates, so both systems stay in sync and help you stay ahead as operations grow more complex. Your Alternative Payments Customer Success Manager can help you choose which system should be primary during onboarding.

Here's how the Business Central integration with Alternative Payments works at setup and across each checkpoint, including any limitations to keep in mind and how it supports business growth for expanding MSP operations:

Where Alti AI fits in the mix

Alti, the financial intelligence inside Alternative Payments, answers questions about your financial operations from your live account. It knows your clients, invoices, payments, and payouts.

Since failed payments don't sync back to Business Central, Alti gives you a faster way to find them. A controller can ask: "Which payments failed last month, card or bank, and what were the top decline reasons?" Alti breaks the payment data down by payment type. Save that question as a weekly Routine Report, which Alti can email to up to 5 teammates. Your reconciliation checklist then starts with a list instead of a search.

Alti also keeps ‘charged’ and ‘deposited’ apart. A successful charge means the money is on its way to you, and Alti can show you the payout that carries it to your bank. Any action that changes your account waits for your confirmation. Alti rolls out to eligible accounts, and what you can do depends on your access level.

Close next month with fewer surprises

When your PSA, Business Central, and your bank disagree at month-end, the cleanup lands on your finance team. That means hours spent matching deposits and reopening invoices, and it delays the numbers you need to run your MSP. A gateway takes the payment, but the right integration carries it through each checkpoint and tells you plainly when something breaks. Month-end becomes a review instead of an investigation.

That’s what the 10-question scorecard is for. Take it into every vendor demo (ours included) and ask each vendor to walk through each checkpoint live. And while you’re at it, test out the vendor’s support team before you sign.

When you're ready to see how Alternative Payments answers each question with your Business Central and PSA setup, book a demo, or browse our integrations.

Frequently asked questions (FAQs)

Does the Dynamics 365 Payment Connector for Adyen work with Business Central?

No. Microsoft built the Dynamics 365 Payment Connector for Adyen for Dynamics 365 Finance, Retail, and Commerce. It suits retailers that sell in-store and online, with card-present payments at a point-of-sale terminal, card-not-present payments from call centers and e-commerce sites, and wallet payments like Apple Pay. Dynamics 365 Business Central uses its own Payment Services instead, and many businesses add a third-party payment integration for business-to-business (B2B) needs like Automated Clearing House (ACH) payments.

What's the difference between a payment gateway and a payment processor?

A payment gateway securely captures a customer’s card or bank details and sends the transaction for approval. A payment processor moves the transaction between the banks and card networks so the money can settle. Neither one, on its own, records the payment in an enterprise resource planning (ERP) system like Dynamics 365 Business Central. That bookkeeping step takes a payment integration, which applies each payment to the right invoice and records the deposit.

How do you tell Business Central apart from Dynamics 365 Finance?

Both Dynamics 365 Business Central and Dynamics 365 Finance are enterprise resource planning (ERP) systems from Microsoft, but they serve different types of companies and use different payment tools. Business Central runs a growing business’s finance and operations in one app. Dynamics 365 Finance belongs to Microsoft’s separate finance and operations apps, built for larger enterprises with more complex, multi-country operations.

To see which one you use, check your address bar. Business Central opens at businesscentral.dynamics.com.