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Handling bank charges that are automatically deducted from a received payment

I invoice a client for $100 worth of services. The client sends me a payment via wire transfer. Unfortunately, the bank deducts a $10 service charge for receiving the wire transfer, and the payment appears on my bank statement as a $90 line (this is a single line on the statement, there are not separate lines for the payment and service charges).

I upload the statement and apply the $90 payment to the $100 invoice in FreeAgent, which then reports that $10 is still owing. Basically, I need to show that the $10 went towards the expense of bank charge. How do I reconcile this?
 
sad I’m confused
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