Best Digital Banking for Nonprofits: Holdings vs. Mercury Compared

For every nonprofit, financial stewardship is mission-critical. Managing donations, grants, team spending, and compliance isn’t just an “admin task”—it’s how you protect your impact and keep trust with funders and your community. In the age of digital banking, a new class of financial platforms has entered the scene, promising to turn what used to be banking headaches into powerful levers for easier, safer, and more transparent nonprofit operations.

Holdings and Mercury are two major contenders in this space. Both are built with the realities of the modern organization in mind: remote teams, digital payments, varied funding streams, multiple programs, and an endless need to show clean, audit-ready records. But for nonprofits especially, not all bank experiences are created equal.

What follows is a nonprofit-centric, plain-English deep dive into both platforms—with an emphasis on real problems, practical features, and the specific needs of organizations that rely on donations and grants to do their good work.

The Nonprofit Banker’s Dilemma: What’s Changed, What Matters

Banking for a nonprofit isn’t like banking for a typical small business. Your team likely juggles:

• Multiple grants or restricted funds

• A mix of cash, check, and digital gifts

• Volunteers and staff making purchases

• Manual approvals to ensure compliance

• Board reviews and external audits

Old-school banks and even many “business bank” options can leave you cobbling together spreadsheets, arguing with fees, and dreading budget season. That’s where digital-first platforms with nonprofit-friendly features come into play.

Table: Features Snapshot for Nonprofits

Understanding Holdings for Nonprofits

No-Fee Banking Matters More

Nonprofit budgets are lean and every dollar must be maximized for your mission—not lost to surprise banking fees. Holdings eliminates the guessing game: no monthly fees, no transaction fees, no minimum balance, and no hidden “monthly service charges.” That means unrestricted, free-flowing movement of your funds, whether you’re issuing 10 reimbursements or 1,000 direct payments this year.

Earn More on Every Dollar

With 2% APY earned across all cash balances—without the need to squirrel money away in separate accounts or meet high minimums—Holdings quietly grows your reserves. This isn’t just nice for interest’s sake; nonprofit leaders know that even a small yield on checking balances can mean more money to deploy for programs year over year.

Segmentation Without Spreadsheets

What really sets Holdings apart is the power to create unlimited “virtual” accounts behind one login. Need to track 12 grants, segregate donor-restricted funds, or manage board-directed reserves? Just spin up a new virtual account in seconds. This keeps every dollar clearly tied to its program or restriction, neatly organized for grant reports or audits, and never mixed up with operational cash.

Real-Time, Jargon-Free Expense Management

Team members—be they staff or volunteers—can receive virtual or physical cards that let them spend securely for field supplies, events, or travel. Administrators set spend limits, monitor every transaction, and freeze or reissue cards instantly. No more collecting receipts in someone’s car or waiting weeks for a reimbursement that derails someone's commitment to the cause.

Full-Service Bookkeeping (If You Need It)

Not every nonprofit has a finance director. Even many $1M+ organizations are running on shoestring staffs. Holdings can match your sophistication by offering optional full-service bookkeeping. The platform supports you whether you just need the basics—that’s automatic categorization, reconciliations, and standardized reports—or want a dedicated bookkeeper to keep you audit-ready.

Easy Grant Reporting, Audit Simplicity

With every banking, spending, and income event automatically tagged to the correct “virtual account,” Holdings makes running grant reports or responding to an auditor a breeze. It’s a world away from sifting through bank statements or struggling to prove to a funder that their restricted gift was spent as promised.

Where Mercury Appeals—and Where It May Fall Short for Nonprofits

Mercury is lauded for its tech-company focus. Startups and global enterprises appreciate its robust API access, meaning software-savvy users can automate custom workflows, create payment dashboards, or even build their own interfaces. For large, venture-backed organizations with in-house developers and complex payment operations, this can be a significant value add.

Mercury also brings impressive FDIC insurance coverage, promising up to $5M protected through partner banks—a compelling feature for organizations managing major endowments or temporarily holding large grant sums.

However, Mercury’s model may not serve nonprofits who need to bank in the physical world (i.e., deposit cash from fundraising events) or who want the flexibility to issue spending cards with the same segmentation and approval controls Holdings enables. Mercury doesn’t support cash deposits, and cash-based teams or those who still handle checks may find this limiting.

Virtual Cards in Action: Nonprofit Spending Made Safer and Simpler

Holdings gives your nonprofit rapid access to both virtual and physical cards. Each can be tied directly to the right virtual account. That means a volunteer buying materials for Program A is spending from Program A’s funds—not Risking accidental commingling of grant-restricted cash.

Why Virtual Cards Matter:

• Instantly issue and deactivate cards to manage volunteers, interns, or one-off projects.

• Set clear daily, weekly, or per-transaction spend limits.

• Monitor usage in real time—so there are no ugly surprises at month-end.

• Eliminate petty cash, paper checks, and the headaches of keeping old “P-card” logs up to date.

For grantees or collaborative partners, it’s easy to onboard them for temporary or recurring spend, with the peace of mind that you can freeze, adjust, or close access as soon as the partnership ends—no forms, no lost cards, no open risk.

Step-by-Step: How to Create and Use Virtual Cards in Holdings

Here’s how your nonprofit can issue and manage virtual cards to simplify operations:

1. Log in to your Holdings dashboard and navigate to the “Cards” section.

2. Select to add a new card, choosing the appropriate program or fund virtual account to pull from.

3. Provide cardholder details (name, email, phone).

4. Configure card settings: name the card for easy tracking (“Grant123 Tech Supplies”), and set daily/monthly spend limits.

5. Save to instantly issue the card. Your team or volunteer receives details securely, ready to spend—online, in person, or wherever Visa is accepted.

6. Monitor activity in real time; freeze, update, or close the card with one click if needed.

Integrations That Respect Your Existing Tools

Finances inside a nonprofit are so much more than just a bank ledger. Board reports, grant applications, and 990s all start with a finance system that’s in sync. Holdings works with Sage Intacct, QuickBooks, and other common accounting tools used by nonprofits of all sizes.

Integration means less duplicate entry, cleaner reconciliations, and no need to export from eight systems just to build a statement for your board or audit. If you’re not ready for full-scale integrations, Holdings also allows simple exports—keeping your team’s preferred workflows in place without demanding a software overhaul.

Bookkeeping for Lean and Growing Teams

Many nonprofits wish for an in-house bookkeeper—but find themselves either outsourcing at great expense or relying on an admin who’s learning QuickBooks after hours.

With Holdings, you can:

• Automate transaction categorization to match your chart of accounts (COA).

• Assign the bookkeeping work to Holdings’ dedicated team, who can handle everything from simple monthly closes to full audit preparation.

• Eliminate the “year-end scramble” for 990s or grantor reporting, since your bank, bookkeeping records, and grant tracking share a single source of truth.

That means you can stay focused on programming and fundraising—not fighting with spreadsheets.

Card Controls Designed for Nonprofits

Deploying the right level of financial control is tough for community-driven teams. You need volunteers empowered to get what they need—within the guardrails that keep your funders and board happy.

With Holdings cards, you:

• Issue cards to individuals, programs, or vendors, ensuring transparency.

• Monitor card usage to prevent budget overruns before they happen.

• Set expiration dates or instantly deactivate a card when a season, project, or staff tenure ends.

• Forget about lost receipts or complex reimbursement paperwork. Every card swipe is logged and categorized on the spot.

Nonprofits who’ve shifted to this model often report a dramatic reduction in staff stress, faster grant spending, and more precise fund tracking. No more “wait, did that coffee shop charge belong to Capacity Building or the Gala?”

Cash Deposits and the Real World

Some nonprofits rely on cash gifts from community events, door-to-door fundraisers, or in-person campaigns. Unlike many digital banks, Holdings enables cash deposits at over 55,000 ATMs—making it simple to get every dollar onto your books quickly, safely, and without risk of mixing personal and organizational assets.

This feature matters if part of your giving base is still cash-reliant, and helps you keep funds in a secure, interest-earning environment from day one.

Built-In Audit Readiness

A compliance-friendly bank is a must for nonprofits. Whether you’re managing federal grants, private foundation dollars, or major donor gifts, transparency and paper trails are non-negotiable.

Holdings:

• Automatically tags every transaction by virtual account—so you can quickly demonstrate how each dollar was received, held, and spent.

• Produces audit-ready reports at the click of a button, organized by program, account, or other custom designation.

• Stores supporting documents, receipts, and reconciliation records in one secure, searchable place.

This makes even the strictest audit or grant review a routine process—not a week-long scramble.

Security and Donor Trust

Your nonprofit is only as strong as the trust it inspires. Holdings uses top-tier data security, including PCI DSS compliance and multi-layer encryption, to keep donor, staff, and financial information safe from threats.

With FDIC insurance up to $3M, every dollar you steward (whether operating funds or temporarily restricted donations) is protected well beyond the industry norm. For most nonprofits, this means you can accept, hold, and disburse significant grants or capital campaign funds without anxiety.

Prioritizing Automation—Without Losing Human Support

Streamlining operations is one of the biggest themes in nonprofit management today. Holdings automates many repetitive financial tasks—from transaction mapping to budgeting and statement generation—so your team spends less time on admin, and more on programs.

But when you need help, real, U.S.-based human support is available to talk you through questions, onboard new teammates, or troubleshoot. The tech works for you; it doesn’t replace you.

When Mercury Might Be the Right Fit

To be fair, Mercury has clear strengths. If your nonprofit is running as a tech-forward entity—with full-time developers ready to build out custom banking dashboards, payment automations, or if you’re holding very large cash reserves (think $2M+) and crave the highest FDIC backing, Mercury’s features are likely attractive.

For nonprofits with major global operations or the need to handle international banking, Mercury’s fee-free global wires and built-in API access may be hard to beat. But if you regularly accept cash donations or depend on “non-software people” being successful right out of the box, Holdings often wins on simplicity and accessibility.

Understanding the True Cost of Banking

Banking fees can eat into even the best-intentioned budgets. Holdings is transparent: no monthly fees, no transaction fees, no wire or ACH fees, and no minimum balance requirements. For nonprofit leaders comparing providers, that means you know exactly what your cost structure is year-round—no surprises, no clawbacks needed.

If your needs grow, Holdings offers affordable, optional add-ons like advanced accounting or full bookkeeping. But the base experience stays truly zero-fee.

Mercury also delivers fee-free banking, but add-ons like invoicing rely on third-party tools (often, Stripe with a fee), and cash-accepting organizations are left out. Their high-yield Treasury product also starts with a $500K+ balance—a hurdle not every nonprofit can reach.

Growing With You—From Startup to Sophisticated Ops

Whether you’re just forming a nonprofit, running programs with a single director and a shoebox of receipts, or scaling with a CFO and advanced approval policies, Holdings meets you where you are.

Start:

• Open with basic, zero-fee banking and simple program segmentation

• Invite board members or volunteers to review spending, with transparent digital logs

Grow:

• Add virtual accounts as you manage more grants or restricted funding streams

• Connect Sage Intacct, QuickBooks, or your preferred toolkit for advanced operations

Advance:

• Bring in full-service bookkeeping for ongoing audit-readiness and peace of mind

• Benefit from reporting and cost allocations at the level of detail demanded by foundation or government grants

Case Study: Simplifying a Grant-Heavy Nonprofit’s Finances

Consider a grassroots organization with eight active grants—all with different requirements, restriction periods, and reporting mandates. With Holdings, each grant lives in its own virtual account. All donations, expenditures, and related documents are captured automatically. Reporting is as simple as choosing the account and exporting the data—no need to backtrack or cross-reference paper bank statements with dozens of Excel tabs.

Every purchase made by staff is tracked to the appropriate project, with card controls ensuring no accidental budget overages or eligibility issues.

Avoiding the Pitfalls of Manual Tracking

Before Holdings, nonprofits often relied on endless spreadsheets, manual bank reconciliations, and email threads about “which project paid for what.” This not only puts your funding at risk but can also slow down vital program activities as teams chase missing documentation or receipts.

By automating reconciliation and tracking through an all-in-one platform, Holdings reduces errors, shortens close times, and keeps executive directors, finance staff, and board members confidently out in front of mission work.

Real-World Flexibility: Compatible, Not Competitive

Holdings doesn’t ask you to abandon what already works. If you love Sage Intacct for reporting, Holdings sends data right over. If your accountant swears by QuickBooks, it’s a native integration. If you just want everything under one roof, Holdings delivers bookkeeping, compliance, and spend management—no need for extra contracts or outside consultants.

This means Holdings is perfectly happy as your only platform or as the connective tissue between your favorite financial tools and your banking experience.

Protecting Mission Dollars, One Feature at a Time

• Segmentation without spreadsheets

• Team spend controls that stop misuse before it starts

• Bookkeeping and reporting designed for boards, funders, and the IRS

• Instant, flexible payments for growing teams

• FDIC insurance that protects large and small orgs alike

You get all the tools, none of the jargon—and you don’t have to change how your nonprofit “does books” just to see the impact.

The Final Word: Who Should Choose Which?

• Nonprofits prioritizing ease of use, program-by-program fund control, and 2% APY on all balances should consider Holdings.

• Teams needing real-time card controls, unlimited cash deposits, and direct accounting integrations find Holdings a perfect fit.

• Organizations seeking optional bookkeeping or all-in-one service—without ditching their favorite accounting tools—will feel right at home.

Mercury is a better fit for those with deep technical capability in-house, who rarely (if ever) handle cash, operate on a global scale, and need access to advanced APIs or $5M+ in FDIC protection for long periods.

Remember, every nonprofit is different—a one-size-fits-all approach doesn’t really fit anyone. Identify your pain points: are you stuck managing program funds by hand, stressed at audit time, fielding staff complaints about reimbursements, or juggling multiple disconnected systems? Holdings exists to solve those, in language your board, accountant, and program staff can all celebrate.

Your organization’s mission deserves best-in-class tools—let your banking platform do the heavy lifting, so you can get back to what truly matters: making a difference.