In Tuscany, starting from the 16th century, chemical observations can be traced in texts on medical practice, botany, alchemy and philosophy, as well as in texts on pharmacopeia, mineralogy and the work of artisans. Along with the Ricettari describing the procedures for preparing medicinals, there was widespread diffusion of the Libri de' Secreti (book of secrets) which gave technical instructions for preparing the substances and colouring agents used in the shops of goldsmiths and artisans. The Pirotechnia (pyrotechnics) by the Sienese Vannoccio Biringuccio, foundry expert and mining engineer, represented the first printed account of the arts that employed fire as a primary processing method. In his famous volume, Biringuccio described techniques for working metals and minerals, the operations of "assaying" gold and silver, forging, distilling, constructing mirrors, ceramics and other alchemistic procedures.

The Medicean Grand Dukes Cosimo I, Francis I and Ferdinand I were especially attentive to chemical experimentation, promoting its development and dissemination. At the Uffizi Gallery and in the Boboli Gardens, laboratories were set up for the production of medicinal substances and for glasswork, activities in which the Grand Dukes themselves liked to engage. The centre of chemical experimentation was, in the early 17th century, the Casino Mediceo di San Marco of Don Antonio de' Medici. In his palazzo, Don Antonio set up a laboratory called the Foundry and a well-furnished chemical library in which he collected a number of hand-written "ricettari". Around the Foundry, Don Antonio brought together numerous scholars, among them Antonio Neri, author of a famous treatise on the art of glassmaking, widely diffused in Europe in the late 18th century. During those same years, Grand Duke Cosimo II had purchased for him in Venice a number of chemical works by the Swiss doctor Paracelsus, which he consigned to the library of the "Giardino dei Semplici" in Pisa. Two Scottish physicians trained in the methods of Paracelsus also worked in Pisa, summoned to Tuscany by Grand Duke Cosimo: Jacopo Macolo, reader in medicine and prefect of the Pisa Botanical Gardens, who may also have been the Grand Duke's personal physician; and Giovanni Macolo, professor of chemistry at the laboratory annexed to the botanical gardens.

In early eighteenth-century Tuscany, chemical research was applied to studying the thermal waters in the Grand Duchy, and to studies in mineralogy and geology. On his journeys of research, Giovanni Targioni Tozzetti detected the presence of mineral deposits in many parts in the region. Giovanni Arduino attempted to inventory the mineral wealth of the Grand Duchy. In 1778 Uberto Francesco Hoefer, the court pharmacist, published a little volume in which he identified the presence of boric acid in the waters of Monterotondo and in those coming from the fumaroles around Pomarance.

The development of Tuscan chemistry in Lorraine times was strictly linked to a policy of institutional reforms promoted by Grand Duke Peter Leopold, who favoured the development of scientific research in the Grand Duchy by establishing research centres and instituting new university chairs. In 1757, at the University of Pisa, the first chair was instituted and was assigned to Nicola Branchi. In 1775, the Museo di Fisica e Storia Naturale was established in Florence, providing a cultural institution suitable for the development of chemistry and its teaching. The Museums' chemistry laboratory, equipped with the most efficient research instruments, today conserved at the Institute and Museum of the History of Science, became a research centre of notable importance for the naturalists of the time. For example, the burning lens constructed by Benedetto Bregans and donated to Grand Duke Cosimo III de' Medici was first used in 1694-1695 by Giuseppe Averani and Cipriano Targioni for experiments on combustion, then in 1814, by Humphry Davy, when he came to Florence with Michael Faraday to conduct research on the chemical nature of the diamond.

The research in pneumatic chemistry and electrochemistry conducted in the laboratory of the Museo di Fisica e Storia Naturale brought Tuscan chemistry into close contact with the research being conducted at the time in the major European scientific centres. The studies of Felice Fontana, then director of the Museum, dedicated to research on carbon dioxide and to perfecting instruments designed to measure the quality of the air, were the first Tuscan contributions to studies on gases. In 1780 Giovanni Fabbroni, Vice Director of the Museum of Physics, published in Paris the Réflexions sur l' état actuel de l' agriculture (reflections on the current state of agriculture) in which he developed new techniques of agronomy and cultivation based on procedures of pneumatic chemistry. Fabbroni's work contributed to the process of applying chemistry to study the plant world, which was emerging at that time in Tuscany and which developed into the disciple of agricultural chemistry. Fabbroni frequently assisted Grand Duke Peter Leopold, who conducted experiments as a hobby, using a special chemical bench and a table of affinities, found today at the Institute and Museum of the History of Science.

In 1807, in the nascent Lyceum of Physical and Mathematical Sciences, instituted at the Museo di Fisica e Storia Naturale, the first chair in theoretical chemistry was inaugurated, along with the teaching of the traditional sciences. The chair was assigned to Giuseppe Gazzeri, a member of the Accademia dei Georgofili, who some time before had lamented the absence of any public teaching of chemistry, institutionalised and financed by the State. This first teaching of non-applied chemistry at the Lyceum continued until the Restoration, when all of the chairs of science existing at the Museum were abolished. With the Restoration the teaching of chemistry was transferred to the School of Pharmacy of the Santa Maria Nuova Hospital and was transformed into a chair of pharmaceutical chemistry. Chemistry continued to be taught in Florence with the institution, in 1813, of a chair of chemistry applied to the arts, at the Technical School of Arts and Manufactured Products in the Arts and Crafts Conservatory, which became the Tuscan Technical Institute in 1853.