If your church is searching for an Aplos alternative for church bookkeeping because the books are three months behind, my verdict comes before you sign anything: a different ledger will probably not fix it. Aplos is not why the October bank reconciliation never got finished. The real problem is that nobody owns the monthly work, and no fund-accounting software on the market does that work for you.
I run a bookkeeping firm, so weigh my view accordingly. But I have watched churches migrate from one platform to another, pay volunteers to re-enter a year of giving, and end up just as far behind in the new system six months later. The software changed. The workflow did not.
So this article does not argue for or against Aplos. It separates two things churches blur together: a ledger (where transactions are recorded) and a bookkeeper (who decides what those transactions mean and proves the numbers are right every month). Once you see the difference, the switching decision gets much simpler.
Is an Aplos alternative for church bookkeeping the right fix for behind books?
Usually not. Fund-accounting software records transactions. A bookkeeper interprets them. When a church falls behind in Aplos, the backlog is almost never missing features. It is decisions nobody has made: which fund a gift belongs to, why the bank balance is off by $412, whether last month's youth camp refund was coded as income or as a reduction of expense.
Use this rough test. If your problems sound like "the software can't do X," you may have a software problem. If they sound like "we haven't gotten to X," you have a people problem, and moving your data somewhere else will not give anyone more time.
- Software problem: your denomination requires a report format Aplos cannot produce, your school and church must run as separate entities with intercompany entries, or your CPA cannot work with your exports.
- People problem: reconciliations are months behind, the undeposited funds account keeps growing, giving statements needed manual fixes in January, or the board report is a bank balance and a guess.
Most churches that ask me about switching are in the second list. I wrote a broader side-by-side in church accounting software vs an outsourced bookkeeper. This piece covers the specific moment when a church has already bought the software and is still behind.
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What Aplos actually gets right
To be fair to the product: Aplos was built for fund accounting from the start. That is more than many churches had when they ran their books in a general-purpose small-business ledger and tracked funds in a spreadsheet next to it. In Aplos you get:
- True fund accounting. Each transaction carries a fund, so fund balances come from the ledger instead of a side file.
- Bank import and a reconciliation module. Transactions come in from the bank, and there is a structured screen for matching them to the statement.
- Donor records connected to the books. Contributions and year-end giving statements come from the same system as the general ledger.
- Nonprofit-shaped reports. Statements that use the net-asset language ("with donor restrictions" and "without donor restrictions") that FASB standardized in ASU 2016-14.
Aplos is also now part of the Velora suite, alongside the Raisely and Keela donor platforms, and it sells its own bookkeeping service in addition to the software. That point matters for this discussion: the company itself recognizes that a ledger alone does not get the work done. Its answer to "we're behind" is to add people, not features.
Why does church bookkeeping stall inside good software?
Four jobs cause most church backlogs. Software supports each one, but none of them happens unless a person does it.
The reconciliation screen is not the reconciliation
A reconciliation module matches bank lines to ledger lines. It cannot tell you why they don't match. Take the most common church mismatch: online giving. Most giving processors deposit gifts net of processing fees. A weekend of $8,400 in online gifts might land in the bank as $8,148.70. If someone records $8,400 of contributions and the bank shows $8,148.70, the reconciliation will never balance. The fix is to record the gross gifts by fund, book the $251.30 as a fee expense, and clear the net amount against the deposit. That takes a person who understands the processor's settlement report. Multiply that by 52 weeks, plus a second processor for the event registration page, and you get the three-month backlog I see most often.
Designated-gift coding is a judgment call
A donor writes "missions" in the memo line. Does that go to the missions fund, the upcoming Guatemala trip, or the general budget line for missions support? Is it donor-restricted or just donor-preferenced? Those answers determine your fund balances, and software cannot decide them. It can only store the answer someone gives it. I explain why most church designations are board-designated rather than truly restricted in designated funds in church accounting. The short version: each gift needs a consistent, documented decision. The best consistency comes from one trained person applying a written policy, not whichever volunteer counts on Sunday.
Nobody closes the month
Closing a month means reconciling every bank and credit card account, clearing the suspense and undeposited-funds balances, confirming each fund balance makes sense, and locking the period so no one posts into it afterward. Aplos lets you lock a period. It does not remind the treasurer that the church credit card has not been reconciled since spring. Churches carry more accountability pressure here than most organizations. Churches are generally exempt from filing Form 990 (the IRS walks through this in Publication 1828, the Tax Guide for Churches and Religious Organizations), so no public return exists for members to check. The monthly close and the monthly board financial report built from it are what hold the finances accountable.
Giving statements inherit every error
IRS rules require a written acknowledgment for any single contribution of $250 or more. When a donor receives something in return for a payment over $75, such as a ticket to a fundraising dinner, the church owes a quid pro quo disclosure. The IRS summarizes both in its guidance on charitable contribution written acknowledgments. Aplos will generate year-end statements quickly, but it prints whatever the ledger holds. A gift coded to the wrong donor, a duplicated check, or an event payment recorded as a pure contribution all end up on a document your members may hand to their tax preparer. That is how bookkeeping errors turn into trust problems. Questions about how a specific gift should be acknowledged are for your CPA or attorney.
How a behind month builds up: an illustrative walk-through
Here is a composite example (not a client) of how a church of about 250 attendees ends up with a clean Aplos subscription and dirty books.
- Week one. Sunday cash and checks are counted by two ushers, deposited Monday, and entered by a volunteer as one lump "general offering" amount. Three checks marked for the building fund are included in the lump sum.
- Week two. Online giving from two processors lands net of fees. The volunteer imports the bank feed and codes the deposits as contributions at the net amount. Fees disappear, and the donor records (at gross) no longer match the ledger.
- Week three. Student ministry collects deposits for a fall retreat through the online registration form. They get coded as contributions, although they are payments for an event, not gifts.
- Week four. Payroll runs through an outside payroll provider. The journal entry that brings it into Aplos is not posted because the volunteer isn't sure how to split the pastor's housing allowance.
- Month end. The reconciliation is off by the fee amount. The building fund balance is understated. The board asks why the retreat line shows a surplus. No one has time to untangle it before the next month starts.
Nothing in that month is a software failure, and moving to another platform fixes none of it. It is five judgment calls that nobody owned. Repeat that for a quarter and you have what churches describe as "Aplos isn't working for us."
When should a church switch away from Aplos?
Sometimes switching is the right answer. It just should not be the first thing you try. These are the situations where I would take a different platform seriously:
- Multiple entities. A church that runs a school, preschool, or separately incorporated ministry may need multi-entity consolidation that a single-organization setup handles awkwardly.
- A CPA or auditor workflow mismatch. If your outside accountant works in a particular platform and your exports cost them hours every year, that friction is real. Talk to your CPA about what they actually need before deciding.
- Church management system integration. If your staff lives in a ChMS for check-in, groups, and giving, and the sync into Aplos keeps breaking, the integration may matter more than the ledger.
- Denominational reporting. Some denominations require specific statistical or financial reports. Confirm the software can produce them before you blame the bookkeeper.
If you do switch, clean the books first. Migrating unreconciled data moves the mess into a new system, and your opening balances will carry every error you had. The sequence in how to switch church bookkeeping providers applies to software changes too: reconcile through a cutoff date, confirm fund balances, then move.
Which should come first: new software or someone to run it?
Someone to run it. Put the person first. Here is the order I recommend to boards and finance committees:
- Name the owner. Decide who is responsible for the monthly close by a specific day each month. That can be a staff bookkeeper, a trained treasurer, or an outside firm, but it has to be one named person or firm.
- Catch up inside the current system. Reconcile every account to a recent month-end, fix the net-deposit problem, and correct fund coding.
- Run three clean closes. Three months in a row of reconciled accounts and a board report delivered on time will show whether the software was ever the constraint.
- Only then evaluate software. By this point you will know which limitations are real, because you have seen the platform used properly.
Separate the duties while you are at it. The person who records transactions should not also be the only person counting cash and approving payments. If your church has not written this down, church financial policies and procedures covers how to divide the roles in a small congregation.
What does an outsourced church bookkeeper do inside Aplos?
An outsourced church bookkeeper works inside the ledger you already have. For most churches, the monthly cycle looks like this:
- Weekly or biweekly: code deposits by fund from the count sheets and giving-processor settlement reports, book processor fees at gross, and flag any unclear designation to the pastor or treasurer instead of guessing.
- Month end: reconcile every bank, credit card, and clearing account; post payroll entries with the correct treatment for the pastor's housing allowance and staff wages; review each fund balance for anything that doesn't make sense; and lock the period.
- Board packet: a statement of financial position, a statement of activities by fund, budget-to-actual, and a short narrative explaining anything unusual.
- Year end: reconcile donor records to the general ledger before giving statements go out, prepare W-2 and 1099 data, and hand organized files to the church's CPA. The bookkeeper does not prepare or sign tax filings; that stays with your CPA.
Clergy payroll is where software-only churches get hurt most. Ministers are employees for income tax purposes but self-employed for Social Security and Medicare, and a housing allowance has to be designated by the board in advance. I cover the mechanics in church payroll and clergy taxes. The specifics for your pastor are a question for your CPA.
This is the work Turnkey CFO does for churches. The software is a tool, and the monthly routine is what keeps the books current. Churches do well when someone owns that routine, whether that is Aplos's own service, a local firm, a trained staff member, or us.
A one-question test before you cancel anything
Ask your finance team: "If Aplos disappeared tomorrow and we moved to the best church software available, who would reconcile the accounts on the fifth of next month?" If the answer is a confident name and a date, go ahead and compare platforms. If people look at each other, you already have your answer, and it isn't a new subscription.
Frequently asked questions
Can Aplos do our bank reconciliation automatically?
Aplos imports bank transactions and provides a reconciliation screen that matches lines to the statement. It cannot explain mismatches, such as giving deposits that arrive net of processor fees. A person still has to investigate the differences and record the correcting entries.
Do we have to leave Aplos to hire an outsourced bookkeeper?
No. Most outsourced church bookkeepers can work inside Aplos, and Aplos also offers its own bookkeeping service. Choose a bookkeeper based on church fund-accounting experience and a clear monthly close routine, not on whether they want you to change software.
Is QuickBooks Online a good Aplos alternative for church bookkeeping?
It can be, if funds are set up carefully with classes and someone keeps the coding consistent. It does not remove any of the monthly work, and fund reporting takes more setup than in a fund-native system. Ask your CPA which format they prefer before switching.
Who should have admin access to Aplos if we outsource?
A church officer, usually the treasurer or executive pastor, should hold the primary admin login. The bookkeeper should have a separate user account. No one person should both record transactions and control cash without someone else reviewing their work.
Does using Aplos mean our church books are audit-ready?
No. Software makes an audit easier to support, but audit readiness depends on reconciled accounts, documented fund decisions, and consistent controls. Whether your church needs an audit or review depends on your denomination, lenders, and board policy, so ask your CPA.