From Payment Runs to Payment Intelligence: What’s Next for Nonprofit Finance

Last year I moved into a new house, and my new utility provider asked for a voided check. I stood there thinking, we still do this? I mailed a piece of paper with my bank account and routing number printed right on it, to a company I’d never met, so they could set up automated billing. It’s a small moment, but it says something about nonprofit finance right now. A lot of the plumbing hasn’t caught up to how comfortable we’ve become with digital payments everywhere else in our lives.

For nonprofit finance teams, payments touch almost everything, from vendor relationships and restricted funds to approvals, donor experience, reconciliation, fraud controls, and audit readiness. For a long time, that meant staff moving invoices, chasing signatures, entering data by hand, printing checks, and reconciling after the fact. That model is changing quickly, not because finance teams want less control, but because they finally have tools that give them more of it.

I’ve been talking with Hallie Hurwitz, who is the Senior Product Manager for payments within Blackbaud Financial Edge NXT^®, about what that shift looks like day to day. Together, we discussed what’s changing on the ground, what to automate first, and where the risk still hides.

Why Payments Feel Like They’re Changing All at Once

Rising digital expectations, more complex transactions, new technology, and more fraud exposure are converging on finance teams who are already stretched thin.

Hallie put the scale of it in perspective. “We have organizations that pay several millions of dollars each month, thousands of payments,” she said. “Imagine handling all of that manually.” Even an electric bill isn’t simple, since plenty of utilities still require a separate slip mailed with payment just to say where the money should go.

Federal Reserve data shows U.S. noncash payments reached 236.6 billion transactions in 2024. Cards accounted for 79% of that volume, ACH for 74% of the value moved, and checks fell to 9.2 billion transactions, just 4% of noncash payments by number.

None of the finance leaders I talk with are implementing automated and AI-powered processes because they want smaller teams. Volume keeps climbing, but the headcount doesn’t.

The Move from Manual Handoffs to Connected Workflows

Nonprofits have always managed complicated payment processes. What’s new is the technology to support them with connected workflows instead of a string of manual steps.

Hallie described payments as covering both sides of the ledger, what an organization pays vendors and what it takes in from constituents. “It’s the approvals to purchase something, figuring out the best way to pay that vendor, the reconciliation, and then posting back to the general ledger,” she told me. “With fund accounting, there are extra layers, like project restrictions and fund restrictions, all the pieces that need to be accounted for correctly.”

That’s what people underestimate if they haven’t managed this firsthand. A nonprofit’s money isn’t one big pool you draw from freely. A single rent payment might get split across a program budget, a grant, and general operating funds. Any step still running on manual data entry is a strong candidate for automation.

So, what starts to disappear with connected payable workflows? Someone stops retyping invoice details that are already sitting right there on the bill. Fewer people walk approval paperwork office to office or log signatures in a spreadsheet. Checks get printed, signed, and mailed less often, and nobody spends an afternoon matching payments back to bank activity line by line or digging through a file cabinet when an audit request comes in.

I don’t think any of that vanishes everywhere on a fixed timeline. It will be more of a shift over time. Staff will move away from printing checks, manual entry, and chasing approvals, and toward exception review, controls, and the judgment calls that actually need a person.

The Bigger Gain Is Control, Not Just Time

Efficiency is the easy sell. The bigger benefit is what automation does for your checkpoints.

Some finance leaders worry that automating payments means giving up oversight. I’d push back on that. Approval checks and balances stay exactly where they are. What changes is how easy it becomes to document them. The right automation doesn’t remove accountability. It makes accountability easier to prove.

Hallie sees this with organizations nervous about accountability and audits. “I’ve heard a lot of nonprofits worry that they won’t pass their audit if they switch to some kind of automation,” she said. “In Financial Edge NXT, every payment run keeps a record of who approved it, how it was paid, and when. Customers we’ve talked to say that visibility has made their audits go more smoothly.”

Instead of wondering after the fact whether you used funds correctly, you already know the allocations are right because they were managed directly in the system.

Risk Is Evolving, So Controls Need to Evolve, Too

Modernizing payments reduces some risk, especially around checks and manual handling. It also raises new questions finance teams need to answer with the same rigor.

The AFP’s 2026 Payments Fraud and Control Survey found that 76% of U.S. organizations experienced attempted or actual payments fraud in 2025. 58% reported check fraud specifically, and business email compromise hit 74% of them. Only 17% used AI to help combat payments fraud. 

Paper checks printed from your organization are an easy target. Once a check leaves your hands, your account and routing number are traveling through the mail, sitting in someone else’s inbox, or waiting in a stack on a desk. A virtual card number never has to pass through the transaction at all, and an EFT payment routed through a vetted partner keeps the real account number out of the process entirely. Third-party bill-pay solutions hide your account and routing numbers, creating an extra layer of protection.

Checks aren’t the only opening. Bad actors also go after vendor relationships directly, impersonating a vendor and asking to redirect payments to a new bank account. Vetted payment partners now validate that submitted account and routing numbers actually match the vendor of record before anything moves, instead of relying on an old-school test deposit. Most organizations can’t build that kind of validation themselves, and if they do, it’s incredibly time-consuming. It has to live inside the payment process.

As donors and vendors expect faster payments, front-end controls matter more. Who can change vendor banking details? How do unusual invoices get flagged? You want smarter friction at the moments that matter.

Humans Stay in the Loop, but at Better Points

I asked Hallie what a best-in-class payments process might look like in five to ten years.

“In the near term, this becomes mostly automated, with humans in the loop at the critical approval points,” she said. “Bills come in automatically, get coded, and route to the right approver, and someone signs off quickly. The system monitors cash flow, pending obligations, and fund restrictions to help build the payment run based on the organization’s schedule—someone reviews, the payment goes out, and it reconciles.”

Longer term, she described something bigger than any one product. A gift comes in, gets allocated to a program or fund, and reaches the accounting team already knowing where it belongs, through to paying the bill it was meant to cover.

This likely begins to change vendor behavior, too. As this becomes automated end to end, even utilities still asking new customers for a voided check will eventually modernize their own intake, and a lot of that friction will disappear on its own.

None of this means removing the person from the process. Fully autonomous accounts payable with no human review isn’t what the evidence points to, and it isn’t where I’d want it to go. The future of payments is a finance team designing the rules, reviewing the exceptions, and trusting the system to handle the repeatable work.

A Practical Path Forward

Look for the overlap between manual effort and risk. That’s where modernization makes the strongest case, and where it’s easiest to justify to your board.

Map the friction. Find where your team still rekeys data, chases approvals, prints checks, or reconciles by hand. Invoice entry, duplicate detection, PO matching, vendor banking changes, check signing, and month-end reconciliation are the highest-value targets.

Start where time and risk overlap. Check reduction, vendor banking updates, payment approvals, and reconciliation are good places to begin. Treat check reduction as both a fraud and efficiency initiative.

Protect the approval moments that matter. Automate routine capture, matching, routing, and payment creation. Keep people reviewing approvals, exceptions, restricted fund questions, and vendor risk.

Update control policies as payment methods change. Vendor change verification, approval thresholds, and fraud escalation steps need to keep pace with ACH and faster payments, not lag behind them.

None of this happens overnight. But start mapping it now, even in small pieces, so you can spend the next few years on the work that needs your judgment instead of the work that just needs your time.

Want to see some of this in practice? Read how updates to Expense Management in Blackbaud Financial Edge NXT are already changing how organizations reconcile incoming funds.