Between 1755 and 1759, Nikolaus von Jacquin was sent to the West Indies and Central America by Francis I to collect plants for the Schönbrunn Palace, and amassed a large collection of animal, plant and mineral samples.
In 1763, Nikolaus von Jacquin became Professor of Chemistry and Mineralogy in Schemnitz (now Banská Štiavnica in Slovakia). In 1768, he was appointed Professor of Botany and Chemistry and became director of the botanical gardens of the University of Vienna. For his work, he was knighted in 1774. In 1783, he was elected a foreign member of the Royal Swedish Academy of Sciences. In 1806, he was created a baron. In 1809, he became a correspondent of the Royal Institute, which later became the Royal Netherlands Academy of Arts and Sciences.
His younger son, Emil Gottfried (1767–1792), and his daughter, Franziska (1769–1850), were friends of Mozart; Mozart wrote two songs for Gottfried to publish under Gottfried's name (K. 520 Als Luise … and K. 530 Das Traumbild) and gave piano lessons to Franziska. Mozart dedicated a considerable number of his works to the Jacquin family, notably the Kegelstatt Trio. This was first played at the Jacquins' house in August 1786 with Franziska playing the piano.
His son Joseph Franz (1766–1839) succeeded him as professor of botany and chemistry at the University of Vienna and wrote several notable botanical books.
Von Jacquin died in Vienna.