The Cessna aircraft crashed into a field at 10.50 am, while attempting to take off from the Lyon-Bron aerodrome, 10 km outside the eastern city, according to local daily Le Progrès.
After coming down in a field in the north-west corner of the aerodrome, the privately-owned plane is believed to have burst into flames. Forty firefighters were sent to the crash site but witnesses told local media that little remained of the body of the plane.
Investigators found three badly burned bodies amid the wreckage, and had earlier been unsure as to the whereabouts of the fourth passenger registered on the flight plan, which had been destined for Aix-en-Provence in the Bouches-des-Rhônes region of southern France.
However, later on this morning, investigators discovered the body of the fourth victim of the crash, elsewhere in the field.
Police have concluded that this passenger was ejected from the plane, according to Le Progrès.
A special air investigation team is already believed to be at the crash site to try and determine the cause of the fatal accident.
Tragically, Tuesday's isn't the first fatal crash in recent weeks to involve a light aircraft travelling from or within France.
At the beginning of September, two British residents were killed when the plane they were travelling in, also a Cessna, crashed off the coast of Jersey, in the English Channel, after taking off from Dinan in western France.
In August, The Local reported how an elderly brother and sister were among three people killed when a tourist plane crashed into a field in Puy-de-Dome in central France.
Just a week earlier, two men were killed instantly when the Cirrus SR20 single-engine aircraft they were travelling in crashed in the Loire region of central France.