QuickBooks Cleanup Checklist (2025 Edition)
Stay organized and accurate-follow our expert-backed checklist to clean up and manage your QuickBooks files efficiently.
Is your QuickBooks account a mess? Whether you're preparing for tax season, onboarding with a new accountant, or simply behind on your books, this checklist will help you clean up your QuickBooks file and get financially organized.
You can follow the steps below or download this checklist as a PDF.
For a complete overview of cleanup workflows, visit our QuickBooks Cleanup Services page or learn about Catch-Up Bookkeeping if you're also behind on monthly reconciliation.
Start With a Backup
- Backup your current QuickBooks file (especially if you're using Desktop)
- Save a dated copy in a secure location (cloud or encrypted drive)
Review Chart of Accounts
- Merge duplicate accounts
- Remove unused or unnecessary accounts
- Categorize expenses properly by type
Reconcile Bank & Credit Card Accounts
- Match transactions to statements
- Investigate unreconciled items
- Reconcile each account through most recent statement
Clean Up Undeposited Funds
- Review undeposited funds account
- Match deposits to sales receipts or invoices
- Clear out old or duplicate entries
Review Accounts Receivable (A/R)
- Run A/R aging summary
- Write off bad debt or very old invoices
- Match payments to open invoices
Review Accounts Payable (A/P)
- Run A/P aging summary
- Match bills to payments
- Void or delete outdated entries
Categorize Uncategorized Transactions
- Search for "uncategorized expense" and "uncategorized income"
- Reassign correct categories using your chart of accounts
- Note recurring misclassifications for future rules
Check for Duplicate Vendors & Customers
- Merge duplicate names
- Standardize naming formats
Verify Payroll Entries
- Ensure payroll is booked correctly by account and class
- Reconcile with payroll provider records (Gusto, ADP, etc.)
Run Reports to Validate Cleanup
- Profit & Loss Statement (monthly and YTD)
- Balance Sheet
- Cash Flow Statement
- Compare with prior year for accuracy
Optional but Recommended
- Set up bank rules for recurring vendors
- Turn on class tracking or location tracking
- Use custom reports to monitor key metrics
When to Get Help
If you're more than 3 months behind, or unsure how to handle historical errors, it may be time to bring in a professional.
At RemoteBooksOnline, we specialize in QuickBooks Cleanup Services. Our certified team can fix, reconcile, and prepare CPA-ready books—fast.
Test Case: Sam's Logistics Company in Ohio
Problem: Sam had 11 months of unreconciled bank statements and misclassified income.
Solution: We completed a full QuickBooks Cleanup and Catch-Up in 14 business days.
Outcome: CPA filed taxes on time with clean reports and Sam saved $2,800 in deductions previously missed.
Want help fixing your QuickBooks fast?
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Explore our QuickBooks Cleanup Services - Need backdated reports too? Check out Catch-Up Bookkeeping
- Learn about all Bookkeeping Services
You can also access this same checklist anytime directly from our QuickBooks Bookkeeping pillar page or through our full Bookkeeping Services hub - making it easier to fix errors or prepare for monthly reconciliation.