David Henderson, 66, has pleaded not guilty to two charges relating to the aircraft crash which killed footballer Emiliano Sala in January 2019.
Henderson appeared at Cardiff Crown Court on Monday via a video link to deny endangering the safety of an aircraft and attempting to discharge a passenger without valid permission or authorisation.
Henderson, of East Riding of Yorkshire, was granted bail and is due to stand trial in October 2021.
David Henderson, 66, a private pilot from Hotham, North Yorkshire, was replaced on the day of the flight by David Ibbotson.
The Piper Malibu PA-46 was en route from Nantes airport in France to Cardiff when it plunged into the English Channel on January 21, 2019.
The 28-year-old Argentine striker's body was recovered on February 7, 2019, and taken to Portland, Dorset.
Mr Ibbotson, 59, has not been found.
A post mortem examination showed Mr Sala died from head and trunk injuries. He had also been exposed to deadly levels of carbon monoxide poisoning during the flight.
It later emerged Mr Ibbotson was not qualified to fly at night.