A QuickBooks cleanup takes a file you can't trust and makes it bank-ready in a fixed sequence: reconcile every account against the statements, empty the "Ask My Accountant" pile, rebuild the chart of accounts for a contractor, and turn on job costing. For most Jacksonville trades businesses, a full cleanup runs two to six weeks — and it only has to happen once.

Here's how to tell whether your file is actually a mess (not just untidy), exactly what a proper cleanup does step by step, and the contractor-specific setup that decides whether QuickBooks tells you the truth about your jobs.

Five signs your QuickBooks is a mess — not just untidy

  • Accounts aren't reconciled. If nobody can name the last month every bank and credit-card account was reconciled to its statement, the numbers in the file are guesses. The balance QuickBooks shows and the balance the bank shows shouldn't be a mystery gap.
  • "Ask My Accountant" is stuffed. That account (and "Uncategorized Expense") is a holding pen, not a destination. When hundreds of transactions live there, your profit-and-loss report is fiction — a chunk of your spending isn't counted anywhere real.
  • There's no job costing. One lump of income, one lump of expenses. You can see whether the company made money, but not which jobs did — which means every bid is priced on a gut feeling.
  • Negative balances that make no sense. A negative bank account, a loan that "grew" backward, a customer who somehow owes you less than zero. These are almost always duplicates or misposted transactions compounding quietly.
  • Duplicate transactions from the bank feed. A feed got disconnected and reconnected, and months of transactions imported twice. Now income is double-counted — and if nobody catches it, you can end up paying tax on revenue you never earned.

Two or more of those and you're past tidying. What follows is the cleanup a good bookkeeper actually runs — knowing it means nobody can hand-wave you.

The cleanup, step by step

  1. Take stock and back up the file. Find the last reconciled month — that's the start line. Everything after it is in scope. Back up before touching anything.
  2. Fix the bank feeds. Confirm every real business account is connected, remove duplicate imports, and pull personal accounts out of the mix. Most feeds only carry a few months of history, so older gaps get rebuilt from statements.
  3. Reconcile every account, every month. This is the spine of the whole job: match every transaction to the bank and card statements until the difference reads exactly $0.00, month by month, through the present. Un-reconciled books are guesses; reconciled books are facts.
  4. Empty "Ask My Accountant." Every parked transaction gets identified and moved to a real category. The account should end the cleanup — and every month after — at zero.
  5. Rebuild the chart of accounts for a contractor. A generic template built for a boutique or a coffee shop will never give you useful numbers. A contractor's chart needs income broken out by type of work, cost of goods sold split into materials, labor, and subs, and overhead kept separate from job costs.
  6. Turn on job costing. Every cost tagged to the job it belongs to, so per-job profit finally shows up on a report. This deserves its own explanation — here's how job costing works for Jacksonville contractors.
  7. Clean up invoices and bills. Ghost invoices customers already paid, bills marked open that were settled months ago, balances that will never collect. The open-invoice list should match reality before the cleanup is called done.
  8. Verify with the reports. A P&L and Balance Sheet that pass the sniff test, and every subcontractor payment flagged so 1099s are a January print job instead of a January scramble.

The contractor-specific part most cleanups skip

A bookkeeper who mostly handles retail or restaurants can reconcile your accounts perfectly and still leave the file useless for running a construction business. The contractor layer is the difference:

  • COGS in three buckets: materials, labor, subs. When cost of goods sold is one lump, you can't see whether a losing job leaked money at the supply house, on the crew, or in sub overruns. Split three ways, the leak has an address.
  • Deposits and draws aren't income yet. A customer deposit for a job you haven't started isn't earned revenue — booked wrong, it makes a month look profitable when it's really a liability you still owe in work.
  • Sub payments tracked all year. W-9s collected up front, payments flagged as they happen — not reconstructed from bank statements the week 1099s are due.
  • Estimates mapped to actuals. Products and services set up so you can lay the bid next to what the job really cost — which is how your next bid gets sharper instead of staying a guess.

Repair the file, or start over?

Sometimes the honest answer is that a fresh file beats a repair: years of unreconciled history, several abandoned cleanup attempts, a chart of accounts remodeled by three different people. In that case a new file with clean opening balances — old file kept as an archive — is often faster and cheaper. A bookkeeper who works in contractor files can tell which path wins within the first look.

Keeping it clean: the monthly rhythm

A cleanup that isn't followed by a routine is a cleanup you'll buy twice. The maintenance is small once the structure is right:

  • Weekly, 15–20 minutes: categorize the bank feed while the jobs are still fresh in your memory.
  • Monthly: reconcile every account, run the job-cost report, and actually read the P&L.
  • Quarterly and year-end: confirm the sub list is 1099-ready and filings are built from reconciled numbers, not estimates.

And if the file has been ignored so long that whole months or years are missing — that's not a cleanup problem anymore, it's a backlog problem. That's what catch-up bookkeeping for Jacksonville contractors is for: the cleanup fixes the file, catch-up fixes the backlog, and the monthly rhythm keeps both from ever coming back.

Seaside Business Solutions rebuilds contractor QuickBooks files like this every week from the Arlington office on Rogero Road — in English and Spanish — for trades across Jacksonville and Northeast Florida. If you're not sure how deep your file's problems go, a free first look will tell you the scope before any work starts.