QuickBooks Cleanup Checklist (Step-by-Step + Free Template)
Use this CPA-designed QuickBooks cleanup checklist to fix reconciliations, undeposited funds, AR/AP, and misclassifications-then close the month with confidence. Download the free template.
If your QuickBooks file is messy-unreconciled accounts, undeposited funds, negative AR/AP-start with a proven process. This QuickBooks Cleanup Checklist is the same step-by-step flow our team uses to deliver CPA-reviewed cleanup projects. Work through each section (recons, categorization, AR/AP, adjustments) and document every fix in the included free template. When you finish the list, you’ll have clean, reconcilable balances, a clear audit trail, and month-end financials your tax CPA or lender can rely on. Prefer to hand it off? Get a firm QuickBooks cleanup quote and we’ll complete the checklist for you-then transition you to a predictable monthly close.
Quick Start - What You Need Before You Begin
Bank, credit card, and loan statements for the cleanup period
Access to your QBO audit log and chart of accounts (COA)
List of connected apps (Stripe, Shopify, payroll, POS)
Aging reports (AR/AP), inventory reports (if applicable)
Target cleanup end-date (e.g., “through last month-end”)
Step-by-Step QuickBooks Cleanup Checklist
Scope & Snapshot
- Identify months of backlog and accounts to reconcile.
- Export current Trial Balance, AR Aging, AP Aging, and Undeposited Funds.
- Record opening metrics in the template.
Bank/Credit/Loan Reconciliations
- Reconcile each account month-by-month to statements.
- Investigate service-charge/interest variances; post missing entries.
- Document unreconciled items and resolutions in the log.
Undeposited Funds & Suspense Accounts
- Match payments to deposits; remove duplicates.
- Clear Undeposited Funds to zero; resolve “Ask My Accountant”/misc suspense.
- Attach support (screenshots, bank proof) in the workpaper folder.
Categorization & Rules
- Normalize vendors/customers; merge duplicates.
- Build bank rules for recurring transactions (ads, SaaS, utilities).
- Reclassify uncategorized income/expense; document bulk changes.
Accounts Receivable (AR)
- Apply payments/credits correctly; remove negative customers.
- Write off uncollectible balances with memo and policy reference.
- Ensure AR Aging ties to the GL at period-end.
Accounts Payable (AP)
- Match bills to payments/credits; remove negatives/vendors with credits.
- Standardize approval flow (maker/checker) going forward.
- Ensure AP Aging ties to the GL at period-end.
Payroll, Sales Tax, and Liabilities
- Tie payroll clearing accounts to payroll reports; fix stale liabilities.
- Verify sales-tax filings/returns; post adjustments where required.
- Attach third-party statements to the month folder.
Inventory & COGS (if applicable)
- Reconcile item quantities/values to inventory system.
- Correct mappings (fees, discounts, shipping) from e-commerce apps.
- Post COGS/adjustments with workpapers.
Adjusting Entries (Accruals, Prepaids, Depreciation)
- Post monthly accruals/prepaids with schedules.
- Record depreciation/amortization per policy.
- Add memo links to supporting schedules.
Go-Forward Monthly Close
- Generate P&L, Balance Sheet, AR/AP Aging; confirm they match subledgers.
- Prepare a variance note (what changed and why).
- Save final Trial Balance and reports to the period folder.
CPA Review & Period Lock
- Have a CPA review reconciliations, JEs, and variance notes.
- Lock the period to prevent back-posting.
- Publish a “clean as of” date in your close calendar.
Free Download - QuickBooks Cleanup Template
Sheet tabs you can mirror in your spreadsheet/Sheet:
Scope - months, accounts, backlog, responsible owner- Recons_Log - account, statement period, variances, status
- Undeposited_Funds - items cleared, deposit dates, reference
- Reclass_Log - before→after accounts, count, reason
- AR_Fixes - customer, doc #, action, proof link
- AP_Fixes - vendor, doc #, action, proof link
- Adjustments - accrual/prepaid/dep entries with schedule link
- Variance_Notes - key drivers vs prior period
- Sign-off - preparer, reviewer (CPA), period-lock date
Common QuickBooks Cleanup Mistakes (and How to Avoid Them)
- Deleting transactions instead of reversing them → Always preserve audit trail.
- Reconciling to bank feed balances → Reconcile to statements, not feeds.
- Ignoring Undeposited Funds → Clear to zero or you’ll double-count revenue.
- Letting AR/AP go negative → Fix applications/credits before tie-out.
- Skipping period locks → Prior months drift; lock after CPA review.
When to DIY vs Hand It Off
DIY fits light backlogs (≤3 months) with few accounts.
Hand it off when:
- 4-12+ months behind, inventory or multi-entity complexity, broken app mappings, or lender deadlines.
Ready to fix the past and close this month?
Get a CPA-reviewed QuickBooks cleanup with a firm timeline.
Frequently Asked Questions
Small backlogs finish in 1-2 weeks; 4-12 months typically take 2-4 weeks. Inventory/multi-entity can add time. We confirm a firm window after a quick review.
Reclassify or reverse-don’t delete-so your audit trail remains intact and reconciliations stay explainable.
Match payments to actual bank deposits (reference dates/amounts), merge duplicates, and post any true adjustments with memos and proof.
P&L, Balance Sheet, AR Aging, AP Aging, and Trial Balance should all reconcile to statements and subledgers for the cleanup period.
Yes—download the template to see our flow, or request a QuickBooks cleanup quote and we’ll complete it end-to-end with CPA review.
After CPA review. Locking prevents accidental edits that break your clean history.
View all answers in our full QuickBooks Cleanup FAQ →
Explore
- Need monthly support after cleanup?
- Historical Reconciliation - Statement-Based Cleanup & Pricing
- Signs You Need a QuickBooks Cleanup (and What It Includes)
- Fix Undeposited Funds, Uncleared Checks & Bank Feed Messes - Fast
- See how our QuickBooks month-end operates
- Behind multiple months? Start with our catch-up scope
- CPA Bookkeeping
- Quickbooks Cleanup