Small business · Cleanup and catch-up
QuickBooks Cleanup and Catch-Up Bookkeeping
We fix books that fell behind and file the returns that went with them. A $500 diagnostic tells you exactly what is wrong and what the fix costs, and the whole $500 comes off the cleanup if you go ahead. Most cleanups run $1,200 to $3,900, depending on how far back it goes.
- CPA led
- Licensed CPA firm in Colorado
- Month to month
- Your books in your own QuickBooks
- Remote, nationwide
Who this is for
Most people who call us are in one of a handful of situations. None of them are unusual and none of them are a reason to be embarrassed.
- The books have not been touched in months and a filing deadline is coming.
- One or more tax years were never filed.
- The bookkeeper quit, or stopped answering, and nobody knows what state the file is in.
- Personal and business spending ran through the same account.
- The company is an S corporation, the owner has been taking draws, and payroll was never set up.
- A sale, a loan application or an investor has put a deadline on clean financials.
- The books were on Bench or QuickBooks Live and that service ended.
- Sales come in through a point of sale system and nothing reconciles to the bank.
If the business holds federal contracts, the work is different and so is the pricing. See government contract accounting instead.
How it is priced
Cleanup pricing depends on facts nobody can see from the outside, so we do not publish a package price and then revise it after we open the file. You pay a fixed diagnostic fee, you get a fixed number, and the diagnostic fee comes off that number.
Diagnostic. A written scope and a fixed cleanup quote, credited in full against the cleanup
Where most cleanups land, once the diagnostic has scoped the work
Of the cleanup fee credited over your first twelve months if you move to a monthly plan
What moves the number
| Driver | Why it matters |
|---|---|
| Months behind | The largest single driver. Each additional quarter is another set of reconciliations, another closing balance to prove, and sometimes another return. |
| Transactions a month | A business running 300 transactions a month costs several times more to catch up than one running 75, over the same period. |
| Payroll | Payroll adds wage reconciliations, quarterly filings and, for S corporations, the owner compensation question. |
| Number of accounts | Every bank account, card and merchant account is a separate reconciliation. |
| Entity type | S corporations and partnerships carry a balance sheet, basis and K-1s that have to agree with each other. |
| Unfiled returns | Quoted separately, per year, once the books for that year are rebuilt. |
We quote a fixed figure in writing before any work begins, and it does not change unless the scope does. All our prices are published.
What the $500 diagnostic covers
The diagnostic is real work, not a sales call. You get a written document whether or not you hire us for the cleanup.
- Every bank, card and merchant account traced to its last reconciled balance, so you know exactly where the books stop being true.
- A list of what is actually wrong, in plain language, not accounting jargon.
- Which tax years are open, which were filed, and which were filed on books that will not support them.
- A fixed cleanup fee, and a fixed fee per unfiled year.
- How long it will take.
If you decide not to proceed, the written scope is yours to take to anybody else. We would rather you have an honest number than an engagement you regret.
What we usually find
Cleanups repeat themselves. These are the issues that come up most often, and all of them are ordinary.
Owner pay handled the wrong way
An S corporation owner who works in the business has to take wages. Draws alone do not satisfy that. Where payroll was never run, the fix is a plan going forward, not a panic about the past.
A point of sale system treated as a ledger
Square, Toast and similar systems record what was sold. They do not hold your cash and they are not a general ledger. A sale recorded with cash tender still needs the cash to be traced to a deposit.
Contractors who should be employees
Paying people on 1099s while controlling their hours, their pricing and their tools is the classification question, and it carries back payroll tax exposure. It gets identified in the diagnostic, not discovered in an audit.
A balance sheet nobody has looked at
Negative inventory, an undeposited funds account that only grows, loans that never amortize, retained earnings that do not tie to the last return. Returns get filed off these numbers.
Sales tax that was collected and never filed
Businesses selling retail product alongside a service often collect sales tax without registering or filing. The exposure compounds quietly.
Personal spending inside the business
The most common of all. It gets separated out rather than deducted, which is both the correct treatment and the one that survives scrutiny.
Catch-up tax returns
Unfiled returns get quoted per year, as a fixed fee, after the books for that year are rebuilt. Filing a return on books that are wrong means amending it later and paying twice.
A few things worth knowing before you call:
- Filing late voluntarily is a far better position than waiting to be contacted. Penalties keep accruing until a return is filed, and first-time penalty abatement is available to taxpayers with a clean prior record.
- We pull your IRS transcripts before quoting, so the plan is built on what the IRS actually has on file rather than what anyone remembers.
- That requires a signed power of attorney, Form 2848, which lets us speak to the IRS on your behalf. You can revoke it at any time.
- State filings and state registrations are handled alongside the federal ones. They are frequently the part that was forgotten.
M2 CPA works with businesses. We prepare an owner’s personal return as part of a business engagement, and we do not take standalone personal returns.
After the cleanup
A cleanup is a one-time engagement and it ends when the books are current and the returns are filed. Nothing obliges you to continue.
Most businesses that got behind once got behind because nobody owned the monthly work. If you want it owned, our monthly plans cover the books, the close, the deadlines and your returns for a fixed monthly fee, with the software billed separately at Intuit’s own price. Half the cleanup fee is credited back over your first twelve months.
Who does the work, and who signs it
Every close and every return is reviewed and signed by a licensed US CPA. Not a bookkeeper, not an account manager, not a rotating team. One licensed person is accountable for the result and you can look the license up yourself.
A named CPA signs
Alexander Mungov, CPA, Colorado license CPA.0030131. Verify it any time through the Colorado DORA license lookup.
A fixed fee, in writing
You get the number before any work starts. It does not change unless the scope does. No hourly surprise at the end.
Your books stay yours
Everything is kept in your own QuickBooks, under your login. If you leave, you take all of it, because it was always yours.
That last point is worth saying plainly. Bench shut down in December 2024 and its customers’ books sat on a platform they did not own. QuickBooks Live has been retired. Firms that keep clients on proprietary systems leave those clients with nothing to take with them.
Common questions
How much does a QuickBooks cleanup cost?
It depends on how far back the books go, how many transactions a month there are, and whether payroll is involved. Most cleanups land between $1,200 and $3,900. The $500 diagnostic gives you a fixed number before you commit, and the full $500 comes off the cleanup fee if you go ahead.
What if I have not filed returns for several years?
That is common and it is fixable. The books get rebuilt year by year first, because a return filed on wrong books has to be amended later. Catch-up returns are quoted per year, as a fixed fee, after the diagnostic shows what each year involves.
Can you work in my existing QuickBooks file?
Yes, and that is the normal arrangement. The books stay in your own QuickBooks Online account under your login. We ask for accountant access, which you can remove at any time.
My bookkeeper stopped responding. Can you take over mid-year?
Yes. We start by pulling the file as it stands and reconciling forward from the last month that actually ties to a bank statement. The diagnostic tells you how much of the year needs rework before the handover is clean.
Do I have to sign up for monthly service?
No. The cleanup is a one-time engagement and it ends when the books are current and the returns are filed. If you want the books kept current afterwards, half of the cleanup fee is credited over your first twelve months of a monthly plan.
I mixed personal and business spending in one account. Is that a problem?
It is the single most common thing we see and it is routine to sort out. Personal spending gets separated out of the business books rather than deducted, and if the company is an S corporation the owner draws get classified correctly so the K-1 and the balance sheet agree.
Related
The 1099 threshold is $2,000 for 2026
Higher threshold, but the same law put cash tips, an occupation code and overtime on the form. File fewer 1099s and your tipped workers lose their deduction.
Prices
Every monthly plan and fixed fee we charge, published up front, with the software on its own line at Intuit’s price.
Is an S corp worth it?
The break-even math on whether an S corporation still pays for itself once payroll and a second return are added.
What online bookkeeping costs
What the national providers charge, taken from their own pricing pages, and what is actually included.
Find out what it will cost before you commit
The $500 diagnostic gives you a written scope and a fixed quote, and the whole $500 comes off the cleanup if you go ahead. Book a call and we will tell you on the call whether a diagnostic is even needed.