QuickBooks vs Aplos: Which Accounting Tool Your Nonprofit Actually Needs (2026)

Verdict: pick QuickBooks via TechSoup if you track only a handful of funds; pick Aplos if restricted grants and audits run your books.

QuickBooks Online via TechSoup costs about $80 a year and does clean books for an org with a few funds, using a workaround for fund accounting. Aplos costs from $79 a month and does true fund accounting out of the box, for orgs juggling many restricted grants or facing an audit. The deciding factor is how many restricted funds and grants you track, not the size of your budget.

Disclosure, separate from the verdict above: we independently review everything we recommend, and we may earn a commission. Today every link on this page is a plain link that earns us nothing; the TechSoup donated QuickBooks plan, which is the right answer for many of you, will never pay us. See how we make money and how we review. Our pick does not change based on who pays.

The short version: which one, and why

Most small nonprofits do not need fund accounting software. They think they do, because their books feel messy, but the mess is usually process, not the tool. If you track two or three funds and want clean reports, QuickBooks Online through TechSoup does the job for about $80 a year. If you track many restricted grants, face a single audit, or need fund-balance reporting your board can actually read, Aplos is built for exactly that and worth its monthly cost.

So the deciding question is not your budget. It is how complex your funds are. Count your restricted grants and your audit exposure, and the answer falls out.

What “fund accounting” actually means, and whether you need it

Fund accounting tracks money by purpose, not just by category. A grant for a youth program and an unrestricted donation are both income, but they cannot be spent the same way, and your board and funders need to see each fund’s balance on its own.

Restricted vs unrestricted income, in plain terms

Unrestricted income is money you can spend on anything that serves the mission. Restricted income is money a funder has tied to a specific purpose or time. Fund accounting keeps a running balance for each restriction, so you can prove a grant was spent the way the funder required.

The honest test: count your funds

Here is our rule of thumb, drawn from practice rather than a study. If you track fewer than roughly fifteen simultaneous grants and you are not subject to a single audit under federal Uniform Guidance, QuickBooks’ workaround usually holds. Past that, the workaround starts costing you more staff time than Aplos costs in dollars, and true fund accounting earns its price.

QuickBooks for nonprofits: what you get, and where it breaks

QuickBooks Online is general accounting software, not a nonprofit tool. Nonprofits adapt it, and for simple books it adapts well.

The Classes workaround for funds

QuickBooks has no native funds. You simulate them with a feature called Classes, tagging each transaction with the fund it belongs to, then filtering reports by class. For a few funds this is genuinely fine, and many small orgs run this way for years without trouble. The ceiling is that QuickBooks reporting is effectively two-dimensional, account by class, so once you need to slice by fund and grant and program at once, you are exporting to a spreadsheet to finish the job. A foundation grant that funds part of one program and part of another, for example, has to be split by hand every reporting period, and the split lives in a spreadsheet the software cannot see. That is the moment the workaround starts costing you.

Grant tracking via custom fields

You can track grants with custom fields and classes, and it works until the grant count climbs. There is no native grant-management view, no automatic restriction releases, and no built-in funder reporting. Small grant loads are manageable; heavy ones become manual.

What auditors ask

An auditor wants to see each restricted fund’s opening balance, what came in, what was released as you met the funder’s conditions, and what remains. In QuickBooks, that statement is assembled by hand from class reports and spreadsheets, because the system does not hold a true fund balance. At low complexity you can produce it in an afternoon. With many grants and a single audit under federal Uniform Guidance, that afternoon becomes a recurring scramble, and the risk of a number that does not tie out grows with every fund. This is the point where the staff time QuickBooks costs you exceeds the dollars Aplos would.

Aplos: what purpose-built fund accounting buys you

Aplos is built for nonprofits and churches, and fund accounting is its core, not a workaround.

Native funds, giving, and 990 help in one place

Aplos tracks restricted and unrestricted funds as real funds, not tags, and produces a balance sheet and income statement by fund out of the box, to nonprofit reporting standards. It also includes donation tracking, online giving forms, donor giving statements, and help with Form 990-N and 990-EZ. The accounting tiers focus on the books; Aplos’s donor CRM and fundraising now sit in its broader Velora suite as separate products, so do not assume the cheapest tier bundles everything.

Where Aplos is genuinely worth the monthly cost

If you manage many restricted grants, report fund balances to a board or funders, or face an audit, Aplos removes the spreadsheet layer QuickBooks forces on you. The system holds each fund’s balance, releases restrictions as you record meeting the funder’s conditions, and produces the by-fund statements an auditor or a board treasurer asks for, without a hand-built reconciliation. For a finance lead at a grant-heavy org, that is hours back every month, a cleaner audit, and one fewer spreadsheet that can quietly fall out of step with the books.

Where Aplos is NOT for you

If you have two or three funds, no audit exposure, and a tight budget, Aplos is paying to solve a problem you do not have. At $79 to $229 a month, plus Gusto for payroll, you would spend four figures a year where TechSoup QuickBooks does your books for about $80. Aplos has also raised prices in recent cycles, and some functions, like check printing, carry an extra cost. Buy it for fund complexity, not for tidiness.

What neither tool includes

Three gaps catch nonprofits whichever tool they pick, so budget for them up front.

Neither includes payroll natively. Both lean on Gusto, priced per employee, as a separate subscription. If you run payroll, that cost lands on top of whichever tool you choose, so compare the all-in number, not the software sticker.

Neither entry tier is a donor CRM. QuickBooks does not track donor relationships or produce giving statements without a separate tool. Aplos includes basic giving records, but its fuller donor and fundraising features now sit in its broader Velora suite as separate products, not in the entry accounting tiers. If you need real donor management, plan a CRM alongside your accounting, not instead of it. Our best CRM for small nonprofits guide covers the options.

And neither replaces a bookkeeper. Software records the numbers, but someone still has to reconcile accounts, code transactions to the right fund, and close the month. The right tool makes that person faster. It does not remove them, and a cheap tool with no one minding it produces expensive messes.

The real cost, both ways

Sticker prices mislead here, because the cheapest correct answer is a donated plan most comparison pages skip.

Option	Real annual cost	What you get
QuickBooks Online Plus via TechSoup	~$80/year admin fee (5 users)	full QBO Plus, fund accounting via Classes, no payroll
QuickBooks Online Advanced via TechSoup	~$170/year admin fee (25 users)	QBO Advanced with more users and reporting, same TechSoup eligibility
QuickBooks Online Plus retail	$1,380/year ($115/mo)	same software, no TechSoup limits
Aplos Lite	~$948/year ($79/mo)	true fund accounting, giving, 990 help, 2 users
Aplos Core	~$1,548/year ($129/mo)	adds budgeting, A/P, A/R
Aplos Advanced	from ~$2,748/year ($229/mo)	adds budgeting by fund and grant, for $250k+ revenue
Payroll (either tool)	Gusto add-on, separate	priced per employee

Pricing verified against techsoup.org and aplos.com/pricing, most recently July 2026.

QuickBooks via TechSoup is about $80 a year. Aplos starts near $1,000 a year before payroll. You pay the difference for true fund accounting, so only pay it if you need fund accounting.

On budget, under $2M with a few funds, go QuickBooks via TechSoup. From $2M to $10M with many grants or an audit, go Aplos, or QuickBooks Online Advanced if you want to stay in the Intuit world; the Advanced plan is also donated through TechSoup, at about $170 a year for 25 users. Over $10M or multi-entity, both are outgrown, so look at Sage Intacct or MIP.

Not sure you qualify for the $80 TechSoup QuickBooks plan, or what else your org can claim? Our discount finder checks your eligibility for donated software and grants in about two minutes. Free.

The QuickBooks Desktop question

If you are still on QuickBooks Desktop, this decision is already on your desk. Intuit retires older Desktop versions on a rolling schedule, dropping security and payroll updates as it goes (Intuit’s discontinuation policy). For many nonprofits, “do nothing” is quietly expiring, which makes this the natural moment to choose the cloud tool that fits.

How to decide in ten minutes

Paste this into a memo for whoever signs off:

• Count your restricted grants and funds. Under ~15 and no single audit, QuickBooks via TechSoup is likely enough.
• Confirm TechSoup eligibility: a 501(c)(3) under $10M budget, one donated subscription.
• If you have many grants, an audit, or a board that wants fund-balance reporting, price Aplos at the tier that matches your revenue, and add Gusto for payroll.
• Whichever you pick, budget payroll separately. Neither includes it.

Our pick

For most small nonprofits, start with QuickBooks Online Plus via TechSoup at about $80 a year. It is the cheapest correct answer, and it pays us nothing, which is exactly why we are comfortable leading with it. If you do not qualify, or you want more than five users without the donated-plan limits, the retail QuickBooks Online plan is the fallback. We independently review everything we recommend, and we may earn a commission. Today this is a plain link that earns us nothing, and it does not change our pick either way.

If restricted grants and audits run your books, pick Aplos at the tier that matches your revenue, and add Gusto for payroll. This is a plain link too, with no commission today; the TechSoup route above, which we recommend first when it fits, will never pay us.

The full disclosure is in how we make money and how we review. For the wider category, see our nonprofit accounting software guide.