In 1906, he joined his friend Anders Christian Jensen-Haarup on a trip to the Mendoza Province in western Argentina in the hope that the arid Andean climate would be beneficial to his health.

The two naturalists made extensive insect collections, which were either sold (e.g. to the German entomologist Heinrich Friese[1]) to cover their travel expenses or were sent to specialists for identification.

[citation needed] Jörgensen's extensive collection activity in understudied regions and his meticulous descriptions of specimens resulted in numerous new species being described by himself and by specialists around the world, with whom he corresponded.

[1] Also the British-American zoologist Theodore Dru Alison Cockerell received specimens from Jörgensen and erected new species based on them.

[3] Two gall midge genera are named for him: Jorgensenia Kieffer, 1913, and Jorgenseniella Maia, 2005 (Diptera: Cecidomyiidae).