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Banking
Thanks for posting here, @tb38,
Joining the thread to share some insights about this negative deposits in the Balance Sheet report.
When you record an invoice payment using the receive payment option or through a bank deposit assigned to the Accounts Receivable, it will post a negative balance in the A/R section of the Balance Sheet.
Please note that the transaction journal of a payment entry debits the bank and credits the A/R account. This means, a reduction to the receivables balance. See this illustration:
If you want to clear the duplicate entry in the Balance Sheet, you need to review the transactions it was applied to. Any changes in there will affect the balances.
You can try deleting the deposit and recreating a single payment, or leave it as is. Journal entries won't resolve this payment posting on reports, it will only fix the balance discrepancies.
Please post here again if you need further help with this. I'll be right here if you need anything else. Message me again to notify me. Have a good one!