QuickBooks Desktop Reconciliation

Your step-by-step guide for accurate reconciliation with QuickBooks Desktop.

This step-by-step guide walks you through reconciling payments in QuickBooks Desktop. It covers the accounts required to select for payments and deposits after connecting QuickBooks Desktop within the Alternative Payments dashboard, and complete bank reconciliation for deposits. Following these steps will help you accurately match bank transactions to invoices and keep your financial records well-organized.

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Configuring Accounts in the Alternative Payments Dashboard

In the Alternative Payments dashboard, you’ll assign three types of accounts:

• Payments Account: Select the "Undeposited Funds" account. This temporarily holds payments until they are reconciled with your bank account.
• Deposits Account: Choose the bank account where Alternative Payments will deposit your payouts.
• Fees Account: Assign an account to track fees if you absorb them on behalf of your customers. If no account is selected, we’ll create one for you, labeled Alternative Payment Fees, to ensure proper recording of all fees.

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Bank Reconciliation Workflow

Step 1: Recording Payments

When a customer makes a payment, we will immediately send the payment and record it to the Undeposited Funds account.

In the example below, you can see that $9,324 has been recorded in the Undeposited Funds account:

When reviewing the payments, you'll notice there are no transaction IDs yet, as the payout from Alternative Payments has not been issued that encompass two invoice payments:

• $8,890
• $444

Step 2: Recording the Deposit

When Alternative Payments issues the payout to your bank account, the funds will be automatically transferred from Undeposited Funds to your bank account.

In the example below, you can see the $9,324 was moved from Undeposited Funds into the NuBank account.

Step 3: Performing the Bank Reconciliation

Now that the funds have been deposited and recorded in QuickBooks Desktop, the payment IDs are now visible within the bank account record:

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Chargebacks and Refunds

If a chargeback or refund occurs after a payment has already been synced and deposited:

• Refunds are recorded as a negative line item in a subsequent deposit
• Chargebacks are deducted from a future payout. Check the Alternative Payments dashboard under Payouts for any chargeback or refund deductions.

Dual-Integration Payment Write-Back

If you are running a dual integration with ConnectWise (CW) as your primary and QuickBooks Desktop as your secondary, this section explains how payment write-back to QBD works — and what does (and does not) affect it.

How Payment Write-Back Works

When a payment is made through Alternative Payments, our system writes the payment back to QuickBooks Desktop by matching on invoice number. Specifically, the invoice number in ConnectWise (your primary integration) must be identical to the invoice number in QuickBooks Desktop (your secondary integration) for the payment push to succeed.

Customer or company name matching between the two systems plays no role in this process. The two matching systems are independent of each other:

• Invoice number matching — determines whether a payment can be written back to QBD. The invoice number must be exactly the same in both ConnectWise and QuickBooks Desktop.
• Customer name matching — used only to sync billing contact data (such as customer email addresses) from the secondary integration. Customer name mismatches do not block or affect payment reconciliation.

This means a partner can have a company named "Acme Corp" in ConnectWise and "Acme Corporation" in QuickBooks Desktop, and payment write-back will still work correctly — as long as the invoice numbers match.

What to Check Before Switching Primary and Secondary Integrations

If you are considering swapping which integration is primary versus secondary (for example, moving from a QBD-primary setup to a CW-primary setup), verify that your invoice numbers are consistent across both systems before making the change. Invoice number parity is the key requirement for payment write-back to function. Customer name discrepancies alone are not a blocker.

Changing which integration is primary is a consequential configuration decision. It affects where invoices and customer data are sourced from, which integration's PDF is displayed, and how billing contacts are synced. We strongly recommend involving your Partner Success or Solutions team before making this change.

Summary

	Invoice Number Matching	Customer Name Matching
Required for payment write-back to QBD?	✅ Yes — numbers must be identical in both systems	❌ No — does not affect payment reconciliation
What it affects	Payment push to QuickBooks Desktop	Billing contact sync (e.g., customer email import)
Impact of a mismatch	Payment will not write back to QBD	Billing contact data will not sync from secondary; payments are unaffected

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By following these steps, you can streamline your reconciliation process and maintain accurate financial records. If you need further assistance, reach out to our Customer Experience team at [e-mail] or via Live Chat in your Partner Dashboard.

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