In 1829 the appointment of Vincenzo Antinori as Director provided the Museum with the opportunity to return to being at the service of science and public education. The birth of new disciplines studying the distribution of animal and plant species in various geographical areas led to a strong increase in the zoological and botanical collections, necessitating a new distribution of the spaces in Palazzo Torrigiani. The “enlightened favour” of Grand Duke Leopold II toward the natural sciences led to the organization in Tuscany of congresses of Italian scientists long before Italian unification. The III Congress of Italian Scientists was held in the Museum In 1841 and that occasion saw the inauguration of the Galileo Tribune, the secular temple dedicated to the great scientist. The Congress agreed on the proposal by the Palermitan botanist Filippo Parlatore for the establishment of a Central Herbarium to gather in one place the Italian local flora and thus favour the exchange of scientific knowledge and specimens. Lodovico Pasini proposed the similar formation of a Central Collection of Italian Minerals and Rocks but it was never realized.
The end of Antinori’s directorship in 1859 coincided with major political upheavals: the fall of the Lorraines, the provisional Tuscan government and the Second War of Independence which initiated the events leading to Italian unification. The Institute of Advanced Studies was founded in Florence in the same year. The Sciences section was established in the Museum, which thus became not only a place of public use of the specimens but also a research laboratory. Teaching took on increasing importance and the museum collections were entrusted to the professors of the respective disciplines.
Under the direction of Cosimo Ridolfi (1860-1865), the Museum played an important role in the large national and universal expositions whose purposes were to present the products of industry, agriculture, crafts and nature to the general public.
The subsequent directorship of the physicist Carlo Matteucci until 1868 caused the Museum many difficulties. Indeed Matteucci, a supporter of the experimental disciplines, was highly critical of the cost of maintaining the natural history collections and the lack of suitable space for research in the La Specola building.