From his expedition to Brazil, he brought to Germany a large variety of specimens of plants, insects, mammals, birds, amphibians and fish.

In 1810, Spix came back to Munich where he sorted the zoological collection and wrote his first publication on starfish and other marine animals.

After this first fundamental publication, a book about the history of zoological classification, published in 1811, he was appointed member of the Bavarian Academy of Sciences.

Spix was also appointed the first conservator, now inline with the title director, of the Bavarian zoological collection, considered as the foundation of the Zoologische Staatssammlung München.

He published several further works, the most important being a comparative morphology of the skulls of many different animals, including men, primates, reptiles, birds, and others.

In 1817, Spix and Carl Friedrich Philipp von Martius travelled to Brazil with a group of Austrian naturalists who accompanied Maria Leopoldina of Austria.

Spix and Martius travelled from southern Rio de Janeiro to northern São Paulo.

Martius travelled by boat to the Yupurá River, and from there he brought to Munich two Brazilian indigenous children from two different tribes, the Juri and the Miranha.

Spix and Martius returned in 1820 to Munich with specimens of thousands of plants, animals, and ethnological objects.

The University of Bamberg, Germany, has established an annual international visiting professorship that carries Spix' name.