# Fix QuickBooks Reconciliation Issues — Causes, Step-by-Step Fixes (QBO & Desktop)

Learn why QuickBooks bank reconciliations don’t match and how to fix them. Step-by-step troubleshooting for QuickBooks Online & Desktop, advanced recovery (undo reconciliation, adjusting entries), prevention tips, and FAQs.

**Summary**

Reconciliation discrepancies in QuickBooks usually come from one of three root causes: incorrect opening/beginning balances, edited/added/deleted transactions that were previously reconciled, or uncleared/duplicate transactions. The fix path is: verify opening balances → run reconciliation reports (Reconciliation Discrepancy / Previous Reconciliation) → find edited/deleted items → correct or re-enter missing transactions → use undo or adjusting entries only as a last resort. For complex or large variances, use Accountant tools or seek a CPA.

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## Why reconciliation problems happen (common causes)

* **Wrong opening / beginning balance** — if the opening balance in QuickBooks doesn’t match the bank’s starting balance for that reconciliation period, the reconciliation will never zero out. This is the single most common cause.
* **Edited, deleted, or newly added transactions that had been previously reconciled** — changing a cleared transaction or deleting it after reconciliation causes a discrepancy. Use the Reconciliation Discrepancy report to find these.
* **Duplicate transactions or bank feed duplicates** — duplicates (manual + downloaded) inflate amounts.
* **Uncleared items and timing differences** — checks or deposits shown in QuickBooks but not yet cleared by the bank.
* **Data entry error**s — wrong amounts, wrong dates, wrong accounts, or currency/exchange-rate rounding.
* **Adjustments and journal entries** (improper use) — prior manual adjustments or an inappropriate reconciliation adjustment can shift balances.

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## Step-by-step troubleshooting

These steps go from least invasive to most invasive.

### 1) Collect your statement & confirm the basics

Pull the bank statement for the reconciliation period (ending balance & date).

Confirm the ending balance on the statement and the ending date you’re reconciling to. Many fixes trace back to an incorrect ending balance typed during reconciliation.

### 2) Verify opening / beginning balance

In QuickBooks Online: go to Accounting → Chart of Accounts → Reconcile and confirm the beginning balance shown. If it’s incorrect, QuickBooks gives steps to fix beginning balance issues.

In Desktop: run Previous Reconciliation and check for balance adjustments (Journal Entries named “Balance Adjustment”). If there’s an unexpected adjustment, investigate who made it and why.

### 3) Run diagnostic reports

Reconciliation Discrepancy (QBO & Desktop) — shows which transactions were changed after reconciliation (edited, deleted, added). This is often the quickest way to locate the culprit.
QuickBooks

Previous Reconciliation report — check which transactions cleared at that statement date.

### 4) Find edited/deleted transactions

Use the Reconciliation Discrepancy report to list transactions changed after reconciling. For any items found: edit amounts back to original (or re-enter the original transaction), or re-clear the correct transaction to restore balance.

### 5) Check for duplicates & bank feeds

Look for transactions that exist twice (manual + downloaded). Exclude or delete duplicates from the bank feed or the register as appropriate.

### 6) Reconcile small differences

For very small differences (e.g., rounding, cents), consider whether a reconciling adjustment (journal entry) is appropriate — but treat this as a last resort because it changes books and can hide root causes. QuickBooks Online has a guided flow for entering an adjusting entry if needed.

### 7) If you can’t find the error: undo & redo

In QuickBooks Desktop you can Undo Last Reconciliation (backup first). In QBO, accountants can use Undo Reconciliation in Accountant tools. If the opening balances are off because of changes in earlier reconciliations, you may need to undo back to a point where balances match and re-reconcile month by month. Use this carefully — always back up the company file or make a copy before mass undos.

## Advanced recovery options

* **Recreate a missing transaction** exactly as it existed at the time (amount/date/payee) and mark it cleared for the statement date — this restores earlier reconciled totals.
* **Investigate journal entries** named “Balance Adjustment” or other reconciliation adjustments; reverse or correct if they were put in incorrectly.
* **Audit trail**: use the Audit Log (QBO) or Audit Trail (Desktop) to identify who changed or deleted transactions.
* **Engage Accountant view / CPA**: large, unexplained differences (> a few hundred dollars or complex months) are safer handled by a qualified bookkeeper/CPA who can trace multi-period impacts and apply safe correcting entries.

> Need guidance? Our QuickBooks experts are available 24/7 at 888-463-3385.