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QuickBooks Reconciliation Tools

Reconciliation Tools: Accurately recording credit card deposits and accounting for fees in QuickBooks 2006


Now it's easier to keep your bank account register in QuickBooks up-to-date. QuickBooks automatically batches your payments for you and tells you when the batch has been deposited in your bank account. You can also download all of your Visa, MasterCard and Discover® Network processing fees in addition to your merchant services fees & adjustments so that your records are more accurate.

Step 1. Deposit credit card payments into your bank account register

  1. On the Customer Menu at the top of the QuickBooks screen, select Credit Card Processing Activities, then deposit credit card payments
  2. When the Payments to Deposit screen opens you can choose to view your deposits by payment types. Payments are also sorted by transaction date.
  3. Click on the Get Funding Status button at the bottom of the Payments to Deposit Screen.
  4. Log-in if prompted.
  5. The Payments to Deposit Screen will be updated with the funding status information for each batch. Funding status may be reported as follows:
    • Funded to bank. This is the date the transaction was funded to your bank
    • Not Funded. This means the batch has not been funded yet as of the time you checked. Check the funding status again the next day to see if updated information is available.
    • Settled. For American Express transactions, "Settled" means the date the batch was processed. QuickBooks Merchant Service only knows when Visa, MasterCard and Discover Network transactions are deposited to your bank account, so a settled batch may not be funded yet. When you deposit a settled batch to a QuickBooks bank account, you should compare it to your bank records to see that the amounts match. If they do not, you also can use the Fees Calculator to account for fees that may have been taken out of your bank deposit total.
    • Unknown. This means you have never checked the funding status of these transactions.
    • Not available. Typically, batches reported as "Not available" have been rejected by the credit card processor, or were posted after the daily cut-off time for processing.
    • Withheld. Batches are withheld for various reasons, typically because fraud is suspected. Once a batch has been "Withheld," it will never be changed to "Funded." You should contact QuickBooks Merchant Service to handle transactions in "Withheld" batches (it is likely that they will contact you first). To remove these transactions so they don't remain in your list of payments to deposit, you can either return to the transaction and delete it, or simply deposit it

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  6. Select the payments you want to deposit in your bank register and click OK to display the Make Deposits window.
  7. Use the Make Deposits window to select the account into which you want to deposit the payments selected in this window.


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Step 2. Account for Merchant Account Fees and for Visa, MasterCard and Discover Network processing fees.

  1. On the Make Deposits Screen, check the box at the bottom of the screen next to After saving go online to assign accounts for merchant account fees and deductions. Alternatively, on the Customers Menu, Download Fees.
  2. You will be taken to the Fees & Adjustments window where you can select the fees, chargebacks and other adjustments you want to account for in your QuickBooks bank and expense accounts.
  3. Click the tab that corresponds to the type of fee you want to account for in your QuickBooks bank and expense accounts.
    • The Summary tab displays all of the types of fees (daily, monthly, other and chargebacks) on a single page. Click the checkbox at the top of the window to select all fees of all types, or click the individual checkboxes to select all fees within a single type of fee.
    • The Daily Fees tab displays daily transaction fees only. Click the checkbox at the top of the window to select all daily fees, or click the individual checkboxes next to each daily fee you want to select
    • The Monthly Fees tab displays monthly transaction fees only. Click the checkbox at the top of the window to select all monthly fees, or click the individual checkboxes next to each monthly fee you want to select
    • The Other Fees tab displays the other transaction fees only. Click the checkbox at the top of the window to select other fees, or click the individual checkboxes next to each other fee you want to select.
    • The Chargebacks tab displays chargebacks only. Click the checkbox at the top of the window to select al chargebacks, or click the individual checkboxes next to each chargeback you want to select.

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  4. From the "Transfer Fee from Bank account" drop-down list, choose a bank account from which you want the selected fees withdrawn. This is typically the bank account into which you already deposited your QuickBooks Merchant Service payments.
  5. From the To Expense Account drop-down list, choose the expense account to which you want the selected fees applied. You might have one expense account for all QuickBooks Merchant Service related fees. Or, you might have a special expense accounts that help you track chargebacks or other type of fees.
  6. Click Enter Transactions to apply the selected fees to the accounts you have chosen.

Step 3:Account for Processing fees for Amex Transactions

  1. From the Banking menu, select Make Deposits.
  2. When the Payments to Deposit screen opens, choose to view deposits by payment method type. Payments are also sorted by transaction date. The reason these are split out is that deposits are made by processors based on payment type and by date. By splitting these batches out for deposit, this more closely matches how the deposits are actually being made into the merchant account's bank account.


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  3. Select the payments you are depositing and click OK to continue. On the Make Deposits screen, select the account you want to deposit the payments into. There are a set of controls near the bottom of the screen under the heading Enter Credit Card Fees. This step is optional but enables you to record any fees that may have been incurred with regard to these payments. (These controls only appear if the deposits selected are all credit card deposits.)


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    1. Enter the actual amount of the deposit made to your bank account in Step 1: Enter bank deposit total. (For example, if the deposit was for $10, but after fees, the amount deposited in your account was $9.60, then enter $9.60).
    2. Click the Calculate button under Step2: Calculate the difference. The difference is the amount in fees that may have been incurred.
    3. From the list at Step 3: Apply the difference to the an expense account used to track your credit card processing fees (you can Add New to create a new expense account for this purpose).
    4. Optionally, enter a memo in Step 4: Enter a memo.
    5. Note that the Deposit Total updates.
    6. Click Save to complete recording the entries. QuickBooks will now accurately reflect the payment your customer made to you, the deposit that was made to your bank and fees that you had incurred for the payments.

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