Skip to main content

How to Reconcile Transactions with QuickBooks Online (QBO) in PayEm

Updated yesterday

The QuickBooks Online (QBO) integration allows PayEm users to reconcile transactions as journal entries, vendor bills & payments; individually or in bulk.

This guide explains all reconciliation methods so you can keep your books accurate and up to date.

⚠️ Important: Always sync your transactions before closing your books. If you sync afterward, you'll need to reconcile in PayEm and in QBO manually.

🗂️ Reconciliation Methods

PayEm supports four reconciliation options:

  • Journal Entry - Posts a single transaction directly to QBO’s ledger

  • Vendor Bill & Bill Payment - Creates a vendor bill and logs a payment against it

  • Bill payment - Creates a full or partial payment against an existing QBO bill

  • Manual Reconciliation - For transactions already entered in QBO or offline subsidiaries

All options (except for vendor bill & bill payment) can be done in bulk

📄 Single Transaction Reconciliation

  1. Go to Activity > Transactions > Ready for reconciliation
    ​

  2. Select the transaction you want to reconcile
    ​

  3. Choose a Sync Method:

Reconcile as a Journal Entry

  1. Select Journal entry > Click Next
    ​

  2. Review or update the Accounting details, and optionally add notes

    • These are auto-filled from the selected card

    • Use dropdowns to choose classification values (e.g., expense account, department)

  3. Click Sync to ERP
    💡 You can also click Save and Exit to pause and return later without syncing.
    ​

What’s Next? - Understanding Sync Status ➡️

✅ Success:

  • Status updates to In process → Sync succeeded
    ​

  • The transaction will move to the Reconciled tab after a successful sync
    ​

❌ Failure:

  • You'll see an error. Fix it and retry, or contact PayEm Support
    ​

Reconcile as Vendor Bill & Bill Payment

  1. Select Vendor bill & bill payment > Click Next
    ​

  2. Fill in the Accounting details and optionally add notes
    ​

    💡 Good to Know:

    • The form prioritizes subsidiary selection

    • Only relevant vendors are shown based on the selected subsidiary

  3. Choose How to Reconcile:
    ​

Option 1: Create New Vendor Bill

A new vendor bill and payment will be created in QBO, with the receipt attached

  1. Select Create new vendor bill
    ​

  2. Fill in:

    • Vendor name

    • Invoice number

    • Date
      ​

  3. Click Next
    ​

  4. Click Sync to ERP
    💡 You can save changes without syncing to revisit later.
    ​

Option 2: Match Existing Vendor Bill

This option allows you to sync a payment to an existing bill in QBO, along with the receipt attached.

  1. Select Use existing vendor bill
    ​

  2. Enter a valid bill ID from QBO > Click Search

    • A confirmation message will appear if it's valid

  3. Click Sync to ERP
    💡 You can save changes without syncing to revisit later.

What’s Next? - Understanding Sync Status ➡️

✅ Success:

  • Status becomes Sync succeeded; links to the bill and payment in QBO are added

❌ Failure:

  • If only the bill syncs and payment fails, the status shows Sync failed.

  • If needed, you can retry the sync or reach out to PayEm Support

Manual Reconciliation (No QBO Sync)

Manual reconciliation is useful when:

  • The transaction is already recorded, or the period is closed in QBO

  • The subsidiary is not connected to QBO

To mark a transaction manually:

  1. Open the transaction

  2. Click Mark as reconciled

What’s Next? - Understanding Sync Status ➡️


The transaction status will update to Manually reconciled and will move to the Reconciled tab

📑 Bulk Reconciliation (Multiple Transactions)

Bulk reconciliation allows you to reconcile multiple transactions at once, saving time and reducing manual work.

⚠️ Prerequisites

  • Select transactions from the same subsidiary only

  • Subsidiary must be connected to QBO for sync to work

  • If the subsidiary is offline, you can only use Mark as reconciled

💡 Good to Know: Transactions are sent to QBO individually, not grouped

How to Reconcile in Bulk

  1. Go to Activity > Transactions > Ready for reconciliation
    ​

  2. (Recommended) Filter by subsidiary (sub-company) before selecting transactions
    ​

  3. Select multiple transactions from the same subsidiary

  4. Choose one of the actions:
    ​

Bulk Sync as Journal Entry

1. After selecting Journal Entry, review and edit the accounting details for the selected transactions
​

Understanding Accounting Details Display ➡️

  • Same values = shown as-is
    ​
    ​Example: The department field is the same in the selected transactions - the department name will show as is in the field
    ​

  • Different values = “Multiple Accounts”


    ​Example: The account is different in each, or in some of the selected transactions - The account field will show the value “Multiple Accounts”
    ​


    💡 In case all values are shown as multiple accounts, it means that there are no missing values, and you can proceed and sync as JE to QBO

  • All empty = blank
    ​
    ​Example: The location field is empty in all selected transactions - The Location field will show blank
    ​

Editing Accounting Details Values ➡️

You can:

  • Leave values as-is (each transaction keeps its own details).

  • Apply a single value across all selected transactions (overrides existing values).
    ​

  • Save changes without syncing to revisit later. This action will edit the field in all selected transactions (bulk edit)
    ​

2. Notice the “Missing details alert” (If it appears) and complete the missing accounting details
​
​Note: Missing accounts may prevent sync
​


3. Click Sync to ERP
​


​

What’s Next? - Understanding Sync Status ➡️

✅ If sync succeeds:

  • Status updates to In process → Sync succeeded

  • Transactions move to the Reconciled tab

❌ If sync fails:

  • An error message explains the issue (e.g., mismatched accounts, currency errors)

  • The transactions remain under Ready for reconciliation

  • You can fix the details and retry, or contact PayEm Support

Bulk Sync as Bill Payment

Use this option to sync multiple payments against the same QBO bill

  1. In the Ready for reconciliation tab, select the transactions
    ​

  2. Select Sync to ERP > Bill Payment
    ​

  3. Enter a QBO Bill ID and click Link
    ​

  4. Click Sync to ERP

    💡 You can save changes without syncing to revisit later.

    This action will edit the field in all selected transactions (bulk edit)
    ​

  5. Update the other fields as usual

Manual Bulk Reconciliation

  1. In the Ready for reconciliation tab, select the transactions
    ​

  2. Click Mark as reconciled
    ​

  3. Status updates to Manually reconciled (no QBO sync)
    ​

🌟 Best Practices for Accountants

  • Always filter by subsidiary before reconciling in bulk

  • Review GL codes, classes, and departments before syncing - overrides apply to all selected transactions

  • Use bulk sync for pre-categorized expenses (e.g., credit card transactions)

  • For offline subsidiaries, use Mark as reconciled after verifying entries in QBO manually

  • Complete reconciliation before the monthly book closure to avoid manual corrections later

Did this answer your question?