[8][9] Despite a recent renovation,[10][11] the museum building was severely damaged in the 2020 Zagreb earthquake and was provisionally declared unfit for use.

[12] In late 2020, the museum holdings were moved to a specialised storage building, pending the completion of repairs to the Amadeo Palace.

Its oldest books were printed in 17th-century Italy, and includes works by Ulisse Aldrovandi, Niccolò Gualtieri and Carl Linnaeus.

In 1875, the museum acquired the large library and natural history collection of Francesco Lanza, a physician and archaeologist from Split, Croatia.

[16] In 1885, Brusina led a successful initiative to publish The Journal of the Croatian Natural History Society (Glasnik Hrvatskoga naravoslovnoga družtva).

[8][19] It also holds the remains of the Neanderthal man found near Krapina by Dragutin Gorjanović-Kramberger, a former director of the National Museum.

[22] The atrium of the museum contains two exhibits: the Rock Map of Croatia (Kamenospisna karta Hrvatske) and the Geological Pole (Geološki stup).

[24][25] Exhibitions at the Croatian Natural History Museum have included "Dormice: in Biology and the Kitchen"[5] and "Lion's Pit", exhibiting the remains of a cave lion (Panthera leo spelaea), found deep in Vrtare Male, a pit cave near Dramalj, Croatia.

With a body length of 3.6 metres (12 ft), the lion was at the time of discovery claimed to be one of the biggest found in the world thus far.

[26][27] Another notable exhibition displayed the reconstruction of a megalodon, an extinct giant shark found in the plains of northern Croatia, where the Paratethys ocean once stood.

[29] In 2009, visitors had the opportunity to view crocodile fossils from the island Pag,[30] while eighty live snakes owned by the Slovenian breeder Aleš Mlinar were exhibited in 2013.