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QuickBooks Cleanup Cost: Price by Months Behind
QuickBooks cleanup at Alignment Capital costs $250 per month behind. See what cleanup covers, what changes the work, and how to request a quote.
In brief
Alignment Capital prices QuickBooks cleanup at $250 per month behind, the same rate as catch-up bookkeeping. The month count is the number of months whose accounts are not fully reconciled, or whose records cannot be relied on, through the last closed period. A 12-month cleanup is $3,000 at that rate. Use the cleanup quote (coming soon) to count the months.
This article is general information, not tax advice.
What QuickBooks cleanup is
Cleanup is the work of making an existing QuickBooks file accurate enough to close. The file already has data. Some of that data is wrong, incomplete, or unreconciled.
Typical problems include:
- Bank or credit card accounts that have not been reconciled to statements
- Duplicated transactions from bank feeds
- A growing Undeposited Funds balance that does not match deposits
- Transfers recorded only on one side
- Opening balances that were never cleared
- Payroll liabilities that do not match payroll reports
- Old uncleared checks and payments
- Transactions in the wrong entity or the wrong account
Cleanup is close to catch-up, and the fee is the same. The difference is the starting point. Catch-up often means months with little or no recording. Cleanup means months that were recorded, but not in a way that ties to statements. Many files need both. See catch-up bookkeeping cost.
What Alignment Capital charges
Cleanup is $250 per month behind.
| Months behind | Cleanup fee |
|---|---|
| 1 | $250 |
| 3 | $750 |
| 6 | $1,500 |
| 12 | $3,000 |
| 24 | $6,000 |
These figures are Alignment Capital's published rate. They are not industry averages.
Monthly bookkeeping after the file is clean is a separate fee, based on annual revenue, starting at $149 a month. Founding-client rates are locked for 12 months. The table is on the pricing page.
Tax filing is not included in cleanup. Returns are prepared by a licensed partner when you request that service.
How months behind are counted in a QuickBooks file
Start with the last month in which every bank, credit card, and loan account was reconciled to a statement, and the reconciliation report still matches that statement.
If the last clean reconciliation is June, and it is now December, six months are behind, including any unreconciled portion of the current month that has already ended.
A reconciliation that was forced to zero with an unexplained adjustment is not a clean close. That month should be counted as behind if the account still does not tie to the statement.
If several years are unreconciled, the month count can be large. The fee is still $250 times the number of months that must be rebuilt or reviewed. The quote will state that count before work starts.
What changes the work inside a month
The stated rate does not change with revenue. The time required inside a month does. These items make a month heavier:
- A high number of bank lines, or several processor accounts
- Inventory, job costing, or billable-time features in use
- Payroll run inside QuickBooks, or payroll run elsewhere and recorded poorly
- Multiple entities combined in one file
- Missing statements, so the reconciliation has no source
- Years of uncleared transactions in Undeposited Funds or opening-balance equity
If reconstruction goes beyond a standard monthly cleanup, the extra scope is identified in the quote. Work does not start without an agreed month count and fee.
How the work is done
Clients connect QuickBooks and their bank on a read-only basis for the initial review. That is enough to see which months are reconciled and which accounts are out of balance.
Cleanup then proceeds month by month, or account by account, until each period ties to statements. The aim is a file a tax preparer can use, not a cosmetic tidy-up of the register.
You keep ownership of the QuickBooks file. Cleanup does not require a change of subscription.
Why cleanup often sits in front of a tax deadline
A partnership or S corporation return is only as good as the books. For calendar-year 2025 Forms 1065 and 1120-S, the federal due date was March 16, 2026. A timely Form 7004 generally extended filing to September 15, 2026. Those dates are in Publication 509 and the Form 1065 and Form 1120-S instructions.
A file with unreconciled accounts delays the return and the Schedule K-1s. Late or incomplete returns can draw a per-owner monthly penalty. See Form 1065 and 1120-S due dates and CP162A late-filing penalties.
Cleanup does not prevent or remove a penalty on its own. It can make the return preparable.
Get a quote
Use the cleanup quote (coming soon). Enter the last clean reconciliation, the number of accounts, and a rough transaction range. The tool returns a month count and a fee.
To continue with monthly bookkeeping after the file is clean, get started or review pricing. For a broader check of whether the books are close-ready, use the books health check (coming soon) when it is live.
FAQ
How much does QuickBooks cleanup cost at Alignment Capital?
$250 per month behind, based on the number of months that are unreconciled or unreliable.
Is cleanup different from catch-up bookkeeping?
The fee is the same. Cleanup starts with a file that already has data. Catch-up often starts with months that were never recorded. Many engagements include both.
Do you need admin access to my QuickBooks file?
No. The review starts with a read-only connection.
What if only one account is out of balance?
The month still needs a close if that account is material to the statements. The quote will count the months that have to be reworked.
Does cleanup include filing my taxes?
No. Tax filing goes through a licensed partner.
Can cleanup be finished before an extended deadline?
That depends on the month count, the condition of the file, and how soon statements are available. Request the quote early. A Form 7004 extension, if still available, extends the time to file, not the time to pay any tax due.