Johnstrup made several geological exploration voyages; 1871 and 1876 in Iceland, 1872 in the Faroe Islands and 1874 in Greenland. In 1876, he led the expedition to Iceland to study Askja and the volcanoes at Mývatn with Þorvaldur Thoroddsen (1855–1921) as his guide.
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He was the founder of the scientific periodical Meddelelser om Grønland which was established in 1878.
In 1888, he led the Geological Survey of Denmark. In 1893, He developed the University of Copenhagen Geological Museum, and led the construction of a new building on Øster Voldgade in Copenhagen.[4]
Johnstrup authored a number of treatises by which he greatly promoted the understanding of Denmark's geological conditions, particularly the glacial phenomena. In 1894, he became an honorary doctorate at the University. In 1892 became a Commander First Class of the Order of the Dannebrog.[4]