When Emperor Franz I dissolved the falconry (Falknerei) in Laxenburg, he bought the collection of Joseph Natterer Sr.

This contained numerous domestic birds, mammals, and insects, and Franz I assigned it the further support and the development of the collection.

Joseph Natterer Sr. introduced both his sons to the collection and taught them the art of preparing skins and mounts.

The director of the collection was Karl von Schreibers and he was assisted by Joseph Natterer junior, who began his career as a volunteer aide and terminated as first curator (Kustos) of the collection, while Johann became, in 1808, a volunteer (freiwilliger) coworker.

From 1802 to 1803, Johann Natterer attended the material academy and heard scientific lectures at the university.

Natterer was initially considered for the expedition leader position but this was given to Johann Christian Mikan and he was selected as the zoologist on the expedition and was accompanied by other naturalists including Johann Baptist von Spix and Carl Friedrich Philipp von Martius.