The QuickBooks Cleanup Checklist

Updated 2026-10

Before you touch anything

• Export the balance sheet and profit and loss for every year affected, so you can see what changed
• Note the last month every account was reconciled; that is where the real work starts
• Disconnect any bank feed or integration you suspect is duplicating, before fixing duplicates
• Give your bookkeeper accountant access rather than sharing a login; it brings the cleanup tools with it

Structure

• Merge or inactivate accounts nobody uses; a chart of accounts should fit on a page
• Create balance-sheet accounts for customer deposits, sales tax payable, each loan and owner equity if missing
• Review every bank rule and delete the ones that code by vendor name alone
• Check products and services map to the right income and cost accounts

Bank and cards

• Reconcile each account month by month from the last clean reconciliation forward
• Remove duplicates as you go; the reconciliation discrepancy report shows what changed after a prior reconciliation
• Clear Undeposited Funds by matching payments to real deposits
• Never force a reconciliation; a plug in Opening Balance Equity is a problem deferred

Coding

• Use Reclassify Transactions (Accountant tools) to move patterns in bulk
• Move customer deposits to the liability account and release them as earned
• Split loan payments into principal and interest; tie each loan to its statement
• Move owner draws and personal spending to equity
• Separate sales tax from sales and tie the liability to what was remitted
• Park anything unidentifiable in a holding account and keep a question list

Payroll

• Match every pay run to the provider’s reports
• Tie payroll liabilities to what was actually filed and paid
• List any missed filings for catch-up

Proof

• A reconciliation report for every account and every month
• A balance sheet that ties: bank, cards, loans, deposits, sales tax, equity
• A profit and loss you can explain line by line
• Opening Balance Equity at zero
• A year-end package for each year covered, ready for the preparer

Where to stop and hand it over

If the last clean reconciliation is more than a few months back, if Undeposited Funds has a balance you cannot clear, if there are two of everything, or if a deadline is closer than the checklist is long, the rest of this list is faster for someone who does it all week. The review is free and tells you which of the above still stands.

Where to go next

• The seven mistakes behind most cleanups
• QuickBooks cleanup services
• Switching from another bookkeeper