In 1779 and 1780, Van Cortlandt was a member of the Court Martial that charged Benedict Arnold with improper conduct while in command of Philadelphia. This was the third time that Van Cortlandt became directly embroiled with Benedict Arnold. This time, the Pennsylvania Provincial Council had accused Arnold of committing eight violations while supervising the city. A Congressional committee determined that some of the charges should be dismissed, others could only be tried in a civil court, and the remainder were subject to review by a court martial. According to Van Cortlandt's memoir, a minority sought to have Arnold cashiered out of the army; instead, he was merely reprimanded by George Washington. It is now known that Arnold was guilty of some of the charges relating to war profiteering, but that a poor case was made against him by the Pennsylvania authorities.