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QuickBooks cleanup: how long it takes, what it costs, and what a good one includes
How to tell you need one
- The bank balance in QuickBooks does not match the bank, and has not for months.
- Undeposited Funds has a balance older than two weeks.
- The balance sheet has negative liabilities, an "Ask My Accountant" account with a balance, or an opening balance equity that never cleared.
- Your CPA extended the return because the books were not ready, or sent a list of 40 questions in March.
- A bookkeeper left, and nobody can say what they were doing.
- You are about to borrow, raise or sell, and someone else is going to read the file.
What a good cleanup includes
| Step | What is done | Why it matters |
|---|---|---|
| File review and written scope | Read every balance sheet account, bank feed and open month; write down what is wrong and a fixed price | No surprises mid-project |
| Chart of accounts rebuild | Industry-standard chart; classes, jobs or locations where they drive decisions | Reports mean something afterward |
| Reconcile every open month | Bank, cards, loans, payroll liabilities, sales tax, merchant accounts | The only proof the numbers are right |
| Fix miscodings and duplicates | Undeposited funds cleared, duplicate bills and payments removed, personal expenses reclassed | The P&L stops lying |
| Tie to the last filed return | Opening balances agree with the tax return; differences explained | The CPA can follow it |
| Cleanup log | Every change dated and described | Audit trail for the CPA, the bank, a buyer |
| Handoff to monthly bookkeeping | Close calendar, connected apps, first weekly cycle | So it never falls behind again |
What it costs
| Where the books stand | Typical price | Typical time |
|---|---|---|
| Current, needs review and fixes | 1x the monthly bookkeeping fee, $500 minimum | 1 to 2 weeks |
| 1 to 3 months behind | 2x to 3x the monthly fee | 2 to 3 weeks |
| 3 to 12 months behind | 4x to 6x the monthly fee | 3 to 6 weeks |
| 12+ months, multiple entities, inventory or crypto | Quoted after a file review | 6 to 10 weeks |
For a company whose monthly bookkeeping would be $900, a six-month catch-up usually lands at $3,600 to $5,400, fixed. Firms that quote hourly for cleanup are guessing too; ask for the fixed number.
Why cleanups fall apart
Most cleanups fail for one of three reasons: the file was reconciled but not tied to the tax return, so the CPA cannot use it; the chart of accounts was left as it was, so the next month is coded the same wrong way; or nobody set up a weekly process afterward, so the file is behind again by the next quarter. ProvenCFO's cleanup service is priced as a project and then hands off to weekly bookkeeping for that reason.
Should you start over with a new file instead?
Sometimes. If the file is more than three years out of reconciliation, has hundreds of unexplained journal entries, or mixes several businesses, a new file with clean opening balances from the last tax return is faster and more honest. The old file stays as an archive. We make that call during the file review and tell you which it is.
Questions people ask
Can you clean up Xero too?
Yes. The steps are the same in Xero and QuickBooks Online, and we have moved clients between them.
Will my CPA accept your cleanup?
Yes, if it is tied to the last filed return and every change is logged. We will walk your CPA through the file directly.
How do I know the cleanup is really done?
Every balance sheet account reconciles to a statement or a schedule, Undeposited Funds is zero or explained, opening balances tie to the return, and the P&L by month makes sense to you. Ask for the reconciliation reports.
Can you clean up and then I keep the books myself?
Yes. Most clients hand off to our weekly bookkeeping because a cleaned file falls behind again fast, but we will quote both.
Written by the people at ProvenCFO who do the work: fractional CFOs, controllers and bookkeepers for American owner-led companies.
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Want this done for your company?
A 20-minute call. We look at how your books run and tell you what we see. Nothing is sold on the call.