In 1768 he was forced to leave Chile due to the Suppression of the Society of Jesus. He settled in Italy where, thanks to his linguistic skills, he obtained the chair of Greek language at the University of Bologna. He soon achieved a good reputation as a historian and geographer, due to his Saggio sulla Storia Naturale del Chili (1778) and Saggio sulla Storia Naturale del Chili (1787). Finally he became a professor of Natural Sciences (1803), given his studies in that area. For example, he published (1782) the Saggio sulla Storia Naturale del Cile, in which he described the natural history of Chile for the first time and introduced numerous species native to that country to science. Furthermore, in that work he is also the first to mention the Paramillos de Uspallata mines, of lead, silver and zinc. All of these works were translated, attracting considerable attention, into German, Spanish, French, and English. In botany, it is regulatory and permissible to simply write "Molina" when a reference is made to any of his descriptions. He also reached the rank of member of the Royal Italian Institute of Sciences, Letters and Arts and the high dignity of the first American academic of the learned Academy of the Institute of Sciences. His fame became more and more notorious, that even Alexander von Humboldt scheduled him a visit.