Flornoy in 1936 became special advisor to the National Museum of Natural History, which sends mission studies and exploration in the Amazon Basin and the Andes.
Many of the monuments discovered, such as those at Piruro, Japallán, Selmín Granero and Susupillo, reveal a type of architecture previously unknown in South America (3- and 4-storey buildings).
Bertrand Flornoy and Marc Corcos discovered the ‘Empire of Yarovilca’, a hitherto unknown pre-Inca civilisation that had not been located since the Spanish conquest (‘Journal de la Société des Américanistes’, 1956: Volume 45, Number 45, Pp 237-238 / 1957: Volume 46, Number 46, Pp 207-226).
According to André Chennevière, Bertrand Flornoy's ‘remarkable work on Amazonia’ has undeniable ‘scientific value’, but is less accessible than that of Ferreira de Castro.
In 1955 he made a sound recording about the Iawa and Bora Indians, which won him the Grand Prix du disque de l'Académie Charles-Cros.