Due diligence fees are most frequently paid through a wire transfer or personal check. Due diligence money is a fee that buyers proffer at the time they make an offer on a home.In essence, it is the buyer's good faith payment to the seller. The first part of your contract timeline is your Due Diligence Period. Due diligence is a non refundable deposit separate from a downpayment which offers the buyer no upside. Understanding due diligence in North Carolina. Learn what it involves and how it protects buyers and sellers during the real estate purchase process. The due diligence fee is a fee paid to the Seller once the contract has been executed, essentially asking the Seller to take their home off the market for you. I put an offer in on a home in NC with due diligence. The same day that my offer was accepted, my husband was arrested.