Boddaert was the son of a Middelburg jurist and poet by the same name (1694–1760). Pieter Jr. obtained his M.D. at the University of Utrecht in 1764 and there became a lecturer on natural history. Fourteen letters survive of his correspondence with Carl Linnaeus between 1768 and 1775. He was a friend of Albert Schlosser, whose cabinet of "curiosities" (natural history objects) he described. In 1783 he published fifty copies of an identification key of Edmé-Louis Daubenton's Planches enluminees, assigning scientific names to the plates. As many of these were the first scientific names to be proposed they remain in use.
In 1785 he published Elenchus Animalium, which included the first binomial names for a number of mammals, including the Quagga and the Tarpan.