Daniel Sennert (1572–1637) elaborated a comprehensive and highly complex natural-philosophical approach, which went far beyond a mere restoration of ancient atomism. As this paper argues, looking at Sennert’s reinterpretation of the traditional notions of “tota substantia” and “calidum innatum” and his radically new understanding of spontaneous generation, Sennert’s natural philosophy was profoundly inspired by his Protestant faith and his pious awe of divine creation but also had a strong empirical component. His atomism was ultimately based on the notion of a hierarchy of forms in animate and inanimate things of nature and on the idea, that the form, as the source of all powers and faculties, can only subsist in a minimal material quantum. When the higher-ranking form perishes, the subordinate form and its matter, which until then served as instrument to the higher form (and, in animate beings, more specifically to the soul) takes over. In this way, the medicinal virtues of (dead) plants, for example, can be attributed to the “calidum innatum” which, during the plant’s lifetime was subservient to the plant’s soul. Sennert’s peculiar interpretation of atomism as a theory of form minima also helped explain way why animal souls—in contrast to the rational human soul—were mortal. If the soul of the animal had been able to subsist in even the most minuscule material corpuscle, it would indeed never have perished and Johannes Freitag would have been right in famously accusing Sennert of heresy because he asserted the immortality of the soul of animals.