At the end of the 19th century, many of the collections housed in La Specola were transferred to other premises
When Filippo Parlatore died in 1877, the Museum no longer had a director and the collections were affiliated to the various scientific institutes. The Zoological Museum remained at La Specola, while the Laboratories of Geology and Palaeontology and of Mineralogy with their respective collections were moved in 1880 to the Piazza San Marco area where they are found today. The Institutes of Chemistry and Physics were moved to premises in Via Gino Capponi.
The Museum of Anthropology, founded by Paolo Mantegazza in 1869, was moved to its definitive site in Palazzo Nonfinito in 1932, while the story of the Garden of Simples (presently the Botanical Garden) is very complex. Founded in 1545 by Cosimo I de’ Medici, it experienced periods of splendour alternating with periods of decline related to its various uses. In 1880 it was assigned to the Institute of Advanced Studies and under the direction of Teodoro Caruel the plants of the Botanical Garden of La Specola were gradually transferred to the present-day site which was completed in 1905.
In 1930 the collections of ancient instruments of Physics and Astronomy were transferred from La Specola to the Institute and Museum of the History of Science, presently the Galileo Museum.
During the 20th century, the Museum underwent a constant decline that can be attributed to excessive reductionism, i.e. the thorough study of ever smaller parts of natural objects which however lost sight of the specimen as a whole. Thus the museum, as a collection of objects, became less important, becoming instead a burden requiring funds and personnel for its maintenance and occupying too much space for the exhibition areas and storerooms. The collections were no longer increased and many rooms were used to house the laboratories and lecture halls required for the growing student population.