Under the Batavian Republic and the Kingdom of Holland he served as a professor of natural history at the University of Harderwijk from 1800 to 1808. After a while he became associate professor of chemistry and pharmacy. In 1808 he appealed to king Louis Bonaparte and was offered work as director of the "to be built" botanical and zoological gardens and museums. In 1808 he became a member of the Royal Institute of the Netherlands. And in 1810 just before the annexation of the Kingdom of Holland by the French Empire, he became professor of natural history in Amsterdam. After the restoration of independence in 1813 and of its colonial empire in 1816, the Netherlands was eager to re-establish contact with its colonies. In 1816 he was offered a position as head of agriculture, arts and science of the colony, and journeyed to the Dutch East Indies where he conducted various botanical investigations throughout the archipelago. Reinwardt was the founder (1817) and first director of the botanical gardens at Bogor (then called Buitenzorg) in Java. There he gathered and cultivated various flora from the surrounding islands such as the Moluccas, Timor and Sulawesi.