In 1756 the Jesuit Leonardo Ximenes founded, on the upper floor of the monastery of San Giovannino, a small astronomical observatory which, after the suppression of the Company of Jesus, was entrusted in 1775 to the Scolopian Fathers. At the death of Ximenes, in accordance with his will, two chairs were instituted, one in astronomy, the other in hydraulics, which remained active up to the middle of the 19th century. In 1813 the activity of weather forecasting was begun, taking its place alongside the traditional studies in astronomy, hydraulics and engineering. Special attention was also dedicated to mathematics, to geodetic surveying and to map-making. In 1830 Giovanni Inghirami made the first "Geometric Map of Tuscany" designed according to modern cartographic standards. In the mid-19th century, its astronomical activity having ceased, the Ximeniano, thanks to the work of Filippo Cecchi and then of Guido Alfani, included seismology among its activities, a discipline that was at that time developing as a science. The work of Cecchi and that of Alfani have significantly contributed to the development of seismology in Italy.

The institution, which has two libraries (an ancient and a modern one) and a historical archive, possesses important scientific collections. The instruments are placed in different rooms, in the same context of use for which they were originally acquired.

The Cecchi Collection, consisting mainly of the instruments used by the Scolopian Fathers Cecchi (seismographs and seismoscopes) and Alfani (mechanical seismographs, photoseismographs, electromagnetic seismometers), constitutes a historical-educational itinerary that illustrates the development of the seismograph from the pioneer apparatus to modern seismographs. The instruments were fabricated in the Observatory starting from 1873 and were used for the research projects undertaken. They include 9 assemblies (seismographs), 42 seismographic instruments, 11 warning systems and seismoscopes.

The meteorological collection is kept in the Meteorology Laboratory and Station, where measurements and research on atmospheric phenomena are carried out at present. It includes instruments used in the Meteorological Observatory starting from 1813 (thermometers, barometers, hygrometers, recording instrumentation, rainfall recorders, and anemographs) and will be supplemented with contemporary devices. All of the instruments have been used – and many of them constructed – in the Observatory. They include 8 barometers, 25 thermometers, and 38 recording assemblies.

The astronomical collection is related mainly to Ximenes, Del Ricco, Canovai, Inghirami, and Antonelli. It includes instruments utilised since the foundation of the Observatory for geodetic activity in the Tuscan territory: binoculars, telescopes, theodolites, geodetic instruments, mixed astronomical and geodetic instruments, compasses, astronomical clocks and regulators in general, technical equipment for geodetic surveying, reproductions of topographic and geographic charts as well as technical drawings. The Telescope Rotunda, with the great reflecting telescope of Tito Gonnella, forms a separate part. The display is arranged according to educational-epistemological principles, to provide a general historical approach to the sector and to illustrate how the scientific activity of the Observatory has always been designed for application to the territory.

Today the Observatory is an independent scientific body of measurement and research, which conducts scientific research in the geophysical and meteorological fields. An institution of Tuscan and national importance, the Observatory has been part of the Seismic Network of the National Institute of Geophysics and Volcanology for over thirty years.