He was premier dancer and ballet instructor at the Opera until 1792. During his time in Sweden, he was described as beautiful as Apollo; "His appearance was of a true Apollo. On top of that he had a form of virtuosity in all kinds of dance, which he used with the finest taste", and his favourite student and dancing partner in Sweden was Charlotte Slottsberg, with whom he made a successful pair in the ballets. He was also active as an actor, a singer and a choreographer; during his stay in Sweden he wrote the ballets Les Meuniers provençaux (1785) and Les Pêcheurs (1789).
He left Sweden in 1792 after the assassination of king Gustav III of Sweden and was employed at the Royal Danish Ballet in Copenhagen in Denmark after a guest performance there. His favourite dance partner in Denmark was Marie Christine Björn, and in 1816-1823 he was ballet master of the Royal Danish Ballet.
Bournonville was married first to the Danish dancer Mariane Jenssen, second to his Swedish house keeper Lovisa Sundberg (the mother of Auguste Bournonville), and he also had a child with the Danish dancer Karen Olsen.