The museum comprises numerous collections on geology, palaeontology, ethnography, natural sciences, and biographical legacies. It manages two temporary exhibition venues, Galerija mežnarija and Galerija klet. Some previous exhibitions include: The Oldest Slovenian Beer and its Story about Julij Stare Brewery from the 19th century in Mengeš and other old breweries in Slovenia; the historical exhibition Settlement Images of Mengeš and Surroundings. Exhibitions of art works created at Jelovšek Art Meeting are regularly on display as well as of different artists such as Lojze Perko, Nataša Prestor, and Miki Muster.
In 2001 the Kranj Regional Office of the Institute for the Protection of Cultural Heritage of Slovenia authorised the Mengeš Museum to supervise machine excavation in town. A total of 16 graves were excavated. They are dated into the period after 600 AD, the stag tine characterising one of them as the grave of an Avar soldier.