With time, all of the Viennese collections experience a steady growth in their inventories, so much that space is at a premium. There is debate on relocating individual collections, but only the receipt of a hand-written note by the Emperor finally raises the hope that the collections will be allocated more space to relieve this situation. It is also was the harbinger of a new era for these collections.
There is considerable interest in information on the natural sciences and the encouragement of this interest seems to have been a concern of the young sovereign: "Dem Reiche der Natur und seiner Erforschung Kaiser FRANZ JOSEPH I" (To the realm of nature and its exploration - Emperor FRANZ JOSEF I) was later to be written on the face of the newly built Imperial Royal Natural History Court Museum, thus documenting the benevolent sentiment of the Imperial Household. Excavations for the construction of this new Museum of Nature started in the fall of 1871, the building was completed ten years later.
On the 29th of April 1876 Emperor Franz Joseph I signs the document certifying the existence of the entity of the Natural History Court Museum. Ferdinand von Hochstetter is appointed as the managing director of the museum. Hochstetter proposes a new organisation for the museum and its collections. Four departments having far-reaching autonomies are to be successors to the older Cabinets; the Imperial Royal Mineralogical Court Cabinet is divided in a Imperial Royal Mineralogical-Petrographical Department and an Imperial Royal Geologic-Paleontologic Department. The petrologist and meteorite specialist Aristides Brezina takes over the management of the former and is supported by the scientific colleagues: Friedrich Berwerth, Rudolf Koechlin and Felix Karrer. The last two named provide voluntary unpaid services. Felix Karrer is Secretary of the Wissenschaftlicher Club (Science Club) and founder of the building-stone collection of the department. By 1886 Köchlin is scientific assistant and later on maintains an inventory of the collection and even keeps a diary.
Hochstetter dies on 18 July 1884 and thus does not live to see the completion of a house for whose founding he had been so actively engaged. His successor as superintendent is Franz R. von Hauer, a geologist and palaeontologist.
In the presence of the Emperor, the new "K.k. Naturhistorisches Hofmuseum" (Imperial Royal Court-museum) is inaugurated on the 10th of August 1889. At first it is open to visitors four days a week - free on Thursdays, Saturdays and Sundays, on Tuesdays for an admission price of one guilder Austrian currency. The house and the collection it contains turn out to be highly popular. From August 13th to the end of December 1889 the museum counted 175,000 visitors, of which 134,000 visited the museum during the 19 Sundays over this time span alone.
During this significant year, the "Mineralogisch-Petrographische Abteilung" (Department of Mineralogy-Petrography) is under the directorship of Aristides Brezina.
In 1889, the renowned collection of William Earl Hidden from Newark (USA) is purchased for a sum of 15,000 fl. with the aid of an advance from the "All highest Family Fund" of the Imperial Household. The repayment of this loan must be repaid in a series of complicated transactions, effected within a time-frame of ten years (i.e. through the sale of mineral doublets, meteorite sections and precious metal redemptions). Unfortunately these redemptions included also samples of silver and gold from the former "Ambrasian Collection" of Archduke Ferdinand II, an irreplaceable loss and impairment to the collection. Despite this, the acquisition of the "Hidden Collection" is of special significance for the Viennese museum. After all, the collection was considered at that time as the second best private mineral collection in the United States, outranked only by the famous Clarence S. Bement Collection, which was later to be acquired by the American Museum of Natural History in New York.
In the same year, several items from the former private collection of Crown-Prince Rudolf, who had committed suicide, were passed on to the department, although apparently this was against his will; the Crown-Prince had left his natural history collection to Viennese teaching institutions.In accordance with these terms, the geologic and palaeontological collection and his mineral collection were to be passed to the "K.k. Hochschule für Bodenkultur" (Imperial Royal University for Agriculture). Instead, the glass imitations of precious stones and some other mineralogical items were entrusted to the Natural History Court Museum.
Koechlin becomes an assistant in 1892 and is promoted to assistant custodian in 1896. In the same year, Friedrich Berwerth is put in charge of the department, taking over from Aristides Brezina, who retires on the 30th of August. Voluntary, unpaid assistance, from 1896 to the end of the Monarchy is provided by Felix Karrer, already mentioned often before, alternately by Anton Pelinka, Hermann Graber, Friedrich Wachter and Karl Hlawatsch. In one last transaction before the collapse of the Monarchy, the museum manages to purchase over the years 1906-07 the magnificent collection of Staatsrath Freiherr von Braun (totalling more than 2,500 items, doublets not included). There follows the far less important collections of August von Loehr, Rudolf von Görgey, although these were not entirely taken into inventory, the delay being due to the war and subsequent poor economic conditions, until after the Second World War (the same happened to the collection of Friedrich Freiherr von Distler, acquired 1932).
A patron of note at the turn of the 19th century is Kommerzialrat Isidor Weinberger. He is one of the great sponsors of mineralogy and the collection of the Court Museum in Vienna is indebted to him for many a beautiful specimen. Thus, the large specimen of amethyst sample from Serra do Mar in Brazil, weighing about 450 kg, donated by him, is today a particularly prominent component and can be admired in front of a side door in hall 3 of the museum. Particularly valuable are the more than 500 meteorite thin sections, formerly in the possession of Aristides Brezina, custodian and former director, which Weinberger was to purchase and later present to the museum.