Spix was born in Höchstadt, in present-day Middle Franconia, as the seventh of eleven children. His childhood home is the site of the Spix Museum, open to the public since 2004. He studied philosophy in Bamberg and graduated with a doctoral degree. Later he studied theology in Würzburg. After attending lectures of the young professor F. W. J. Schelling, Spix became interested in nature. He quit his theology studies and began studying medicine, which he finished with a second doctoral degree in 1807.
After a short time working as a physician in Bamberg, he was appointed by king Maximilian I Joseph of Bavaria as student ("Eleve") of zoology in Munich at the Bavarian Academy of Sciences and Humanities in Munich in 1808. He received a scholarship to go to Paris to learn scientific zoology with Georges Cuvier and others. From there he also made a first excursion to the sea coast of Normandy in Northern France. Later he travelled to Southern France and Italy, collecting animals for the zoological collection of the Bavarian Academy of Sciences and Humanities and investigating marine animals.
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, apes, reptiles, birds and others. This book, the Cephalogenesis, published in 1815, was written in Latin and illustrated with beautiful lithographs.