Around 1599 he became interested in alchemy and attempted to create an alchemical concordance, synthesizing the works of different authors. In 1608 he went to Prague, and on 19 September 1609 he formally entered the service of Rudolf II as his physician and imperial counsellor. Ten days later, Rudolf raised him to the hereditary nobility and gave him the title of imperial count palatine. Around this time, Maier published an extremely limited print run of De Medicina Regia et vere Heroica, Coelidonia (1609), including in it his autobiography.
His Atalanta Fugiens, an alchemical emblem book, was published in 1617. Alongside images, poems, and discussion, it included fifty pieces of music in the form of fugues, the form itself being a pun on Atalanta "fleeing". In 1619 Maier became the physician of Landgrave Moritz of Hesse-Kassel (or Hesse-Cassel). In 1620 he moved to Magdeburg to practice medicine, where he died at the age of 54, leaving a noteworthy quantity of unpublished works.
A devout Lutheran all his life, Michael Maier had a strong influence on Sir Isaac Newton. He was also involved in the Rosicrucian movement that appeared around this time, which afforded part of the matter of his Themis aurea.
Atalanta Fugiens (Atalanta in flight) is an emblem book by Michael Maier (1568-1622), published by Johann Theodor de Bry in Oppenheim in 1617 (2nd edition 1618). It consists of 50 discourses with illustrations by Matthias Merian, each of which is accompanied by an epigrammatic verse, prose and a musical fugue. It may therefore be considered an early example of multimedia."