QuickBooks Cleanup Checklist – A Step-by-Step Guide to Fix Your Books

Messy QuickBooks files are more common than you think – but they don’t have to stay that way. Whether you’re months behind or dealing with reconciliation issues, this QuickBooks cleanup checklist will help you get your financials back on track fast.

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At Remote Books Online, we use this very process when helping businesses across the U.S. clean up their QuickBooks – so it’s field-tested and CPA-approved.

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QuickBooks Cleanup Checklist

  • Backup Your Data
    Always start by saving your current file. If you’re using QuickBooks Online, export key reports and bank registers.
  • Review the Chart of Accounts
    Clean out duplicates, merge irrelevant accounts, and realign your categories to match your tax structure.
  • Categorize Unassigned Transactions
    Go through your bank feeds and assign categories for any uncategorized income or expense items.
  • Reconcile All Accounts
    Match each bank and credit card statement with your QuickBooks records – month by month if needed.
  • Fix Undeposited Funds
    One of the most common issues! Make sure all sales receipts and payments are tied to actual deposits.
  • Correct Misapplied Payments and Vendor Balances
    Check for duplicate payments, unapplied credits, and open balances that should be cleared.
  • Run Reports and Cross-Verify
    Generate a Profit & Loss, Balance Sheet, and A/R Aging report. Look for red flags like negative balances or odd swings.
  • Document What You Changed
    Keep a cleanup log (date, correction, reason) – it helps for tax prep and future audits.

Want Help from a Pro?

If this checklist feels overwhelming, don’t worry – our expert bookkeepers can do it for you. We offer QuickBooks cleanup services tailored for your business, whether you’re behind by 2 months or 2 years.

Get your QuickBooks back in shape – request a quote and let us clean it up fast and CPA-ready.

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Our QuickBooks cleanup checklist is trusted by clients in Los Angeles, CA 90001 and Dallas, TX 75201, helping them fix errors, reconcile accounts, and stay tax-ready.

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Take control of your business finances with confidence! Our detailed brochure provides insights into how Remote Books Online can help you maintain accurate bookkeeping, stay tax-ready, and make informed financial decisions. Discover how our tailored bookkeeping services can support your business growth and simplify your financial management.