One of the main activities of the museum is the preservation of specimens maintained and stored in the various museum sections. Each depository includes 165 storage locations which contain the bulk of the museum’s main and exchange samples.

The sections consist of donations, private collections as well as purchased and exchanged samples. Between 500 and 1 000 specimens arrive at the museum each year. As of January 2016, the museum maintains more than 31 000 items, classified in the following categories:

•  “Minerals of the Earth” – the most extensive mineral collection on the Balkans, including more than 7 800 specimens of 1 663 mineral species.
• “Mineral Resources of the Earth” – various genetic types and industrial minerals from over 106 countries.
• “Minerals of Bulgaria” – the most complete collection of Bulgarian minerals – a total of 4 600 mineral specimens.
• “Mineral Resources of Bulgaria” – includes 3 400 specimens collected from more than 100 locality.
• “Materials” – a total of 2 600 items divided into 20 topics.
• “Scientific Collections” – more than 600 specimens including personal samples of newly discovered minerals.

Several collections include specimens from multiple sections:

• Collection “Giant Crystals” – one of the two largest crystal collections in the world.
• Collection “Gemstones” – includes almost 3 000 mineral specimens representing almost all of the currently known minerals with gemstone characteristics.

The museum has 1663 of the world's 5,780 mineral species.

From 1990 to 2021 the museum has organized 55 visiting exhibitions of mineral samples, 2 of which abroad.
All primary and exchange items are documented in the museum’s inventory books as well as the inventory database available since 1996. All newly arrived items are promptly entered into the database which is also used to track the items’ locations.