QuickBooks Cleanup Services
A QuickBooks file can balance and still be wrong about everything that matters. A cleanup finds what is wrong, fixes the structure that let it happen, and recodes the history so the reports mean something. The file you already have is usually the starting point, not the problem.
What a QuickBooks cleanup is, and is not
It is not starting over. Most files that arrive for cleanup are salvageable: the customers, vendors and items are fine, the chart of accounts needs trimming, and the transactions need recoding. Starting a new file throws away the parts that were right and leaves the old problems in a file somebody will still open.
A cleanup works in the file you have. Your bookkeeper reviews it, writes down what is wrong, fixes the structure, then works through the history month by month until every account reconciles to its statement. Where a file is genuinely beyond repair, usually because of years of duplicated bank feeds, they say so and quote a rebuild from the bank instead. That is rare, and you will be told which you are looking at before anything is agreed.
How it is quoted
Read access first. Your bookkeeper looks at the file and the bank statements, measures how many months are affected, how many accounts, how many transactions and whether payroll was run, and comes back with a written quote for the project. The structure is a deposit up front, a monthly retainer while the work runs, and then ordinary monthly bookkeeping from $250 once the file is clean.
If there is a date, say so in the request. A cleanup against a tax deadline is worked in a different order, current year first, and the quote says plainly whether the date is reachable.
The seven things found in almost every file
- Undeposited Funds holding months of customer payments, so invoices show paid while the bank shows nothing, or deposits appear twice
- A bank feed connected twice, or an integration pushing deposits that were also imported, doubling income
- Customer deposits and retainers posted as income the day they arrived, rather than as a liability released when earned
- Loan and equipment payments expensed whole, so the loan balance never falls and profit is understated by the principal
- Owner draws, personal purchases and transfers between accounts coded as expenses
- Sales tax collected sitting in income, with the remittance later coded as an expense
- Opening Balance Equity carrying a number nobody can explain, usually from a migration or a reconciliation that was forced
None of these shows up as an error. The file balances, the reports run, and the profit on the screen is wrong by the sum of all of them. The seven-mistakes guide describes the symptom of each so you can check your own file.
The order of work
Structure first
A chart of accounts that fits the business, with the fifty accounts nobody used merged or made inactive. Balance-sheet accounts for deposits, loans, sales tax and owner equity. Bank rules reviewed and the bad ones deleted, because a rule that codes every Amazon purchase to office supplies will keep doing so.
Then the bank
Each bank, card and loan account reconciled to its statement, month by month, from the last clean reconciliation forward. Duplicates removed, missing transactions added, Undeposited Funds cleared against real deposits.
Then the coding
Transactions recoded in bulk where a pattern is wrong and one by one where it is not. Deposits and loans moved to the balance sheet. Owner activity moved to equity. Sales tax separated from sales. Anything that cannot be identified from the bank goes to a holding account and a short list of questions, rather than being guessed.
Then the proof
A reconciliation report for every account and every month, a balance sheet that ties to the statements, and a profit and loss that can be explained line by line. That package is what goes to your tax preparer.
What to have ready for the first look
- Accountant access to the QuickBooks file, which you grant from the Manage Users screen in a minute
- Read-only online access to each bank and card account, or the statements for the months in question
- The last month you believe the file was right, if there was one
- Whether payroll was run, and through which provider
- Any date in view: a return, an extension, a loan application, a sale
Nothing else is needed to measure the job. Receipts, if they matter, are requested later and only for transactions where they change the coding. The people who never start a cleanup are usually the ones who tried to gather everything first; the first look needs access, not a finished archive.
QuickBooks Online and Desktop
Online is where most cleanups happen now, and its Accountant tools (reclassify transactions, the reconciliation discrepancy report, the audit log) are built for this work. Desktop files are cleaned up too; the mechanics differ but the order of work is the same. If you are on an old Desktop version, note that Intuit no longer sells new Desktop subscriptions to US customers apart from Enterprise, so a move to Online is worth planning. A cleanup is the right moment for it, because the migrated file starts clean rather than carrying the problems across.
Payroll run through QuickBooks Payroll, Gusto or another provider is reconciled to the filings. Where filings were missed, that is said plainly and handled as part of the project.
What it costs
Every cleanup is quoted after a look, because the range is wide. A few months of a one-person business with one account is a modest project. Two years of a company with three cards, payroll and a doubled bank feed is not. The deposit, retainer and monthly structure is the same for both, and the cost guide gives worked examples at several sizes.
The ongoing fee once the file is clean starts at $250 a month and depends on transaction volume and whether payroll is included.
Send how many months are affected, how many accounts, and whether there is a date. The reply within a business day says what the deposit would be and whether the date is reachable.
| Report | Before the cleanup | After |
|---|---|---|
| Bank balance in QuickBooks vs the bank | Off by an amount nobody can explain | Matches, with a reconciliation report for every month |
| Undeposited Funds | Months of payments sitting in it | Zero, with every payment matched to a real deposit |
| Customer deposits | In income the day they arrived | On the balance sheet until the work is done |
| Loan balances | Unchanged for a year | Reduced by every principal payment, interest expensed |
| Owner draws | Scattered through expenses | In equity, where the tax preparer expects them |
| Profit and loss | A number that does not match the bank | A number that can be explained line by line |
Common questions
Will my file be started over?
Almost never. The existing file is reviewed and repaired in place. A rebuild from the bank is quoted only when a file is beyond repair, and you will be told which before anything is agreed.
How long does a cleanup take?
A few months of one account can be days. A multi-year file with payroll is weeks. The quote includes an honest timeline, and a deadline changes the order of work rather than the total.
Do I need the Accountant version of QuickBooks?
No. Your bookkeeper is given accountant access to your file, which brings the cleanup tools with it at no cost to you.
What if I am on an old Desktop version?
It can be cleaned up as it is. If a move to Online makes sense, the cleanup is the right moment, so the migrated file starts clean.
Will my previous bookkeeper need to be involved?
No. The file and the bank statements are enough. If they are willing to hand over notes, that helps; it is not required.
What happens at year-end?
Your bookkeeper prepares a year-end package for your tax preparer for every year the cleanup covers, so returns can be prepared from real numbers.
What about after?
The file rolls into monthly bookkeeping at the ordinary fee, with the structure fixed so the same problems do not come back.
Related services
- Catch-Up Bookkeeping Services
- Bookkeeping Cleanup Services
- Behind on Bookkeeping Before a Tax Deadline
- Multiple Years of Bookkeeping, Rebuilt
- Monthly Bookkeeping After the Cleanup
Who this is for
Request a quote for quickbooks cleanup
Tell us how far behind the books are and whether there is a date. Your bookkeeper replies within one business day with a plain answer: what it would take, whether the date is reachable, and what the deposit would be. Requests answered within one business day · Calls Mon–Fri, 9am–5pm Eastern Or call (888) 786-6502 if you would rather talk it through first.