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Chemistry
The best of Stahl’s work in chemistry was done while he was a professor at Halle. Just like medicine, he believed that chemistry could not be reduced to mechanistic views, since, according to Stahl, chemical qualities should be described with purely chemical views and theory. Although he believed in atoms, he did not believe that atomic theories were enough to describe the chemical processes that go on. He believed that atoms could not be isolated individually and that they join together to form elements. Depending on the types of reactions that took place during these formations, and what was produced, substances could be organized with relative affinities. He took an empirical approach when establishing his descriptions of chemistry. His work in Germany aligned with that in France as he worked to distinguish chemistry, mechanism, and medicine.

Stahl used the works of Johann Joachim Becher to help him come up with explanations of chemical phenomena. Becher's theories attempted in explaining chemistry as comprehensively as seemingly possible through classifying different earths according to specific reactions. Terra pinguis was a substance that escaped during combustion reactions, according to Becher. Stahl, influenced by Becher's work developed his theory of phlogiston. Phlogiston theory did not have any experimental basis before Stahl worked with metals and various other substances in order separate phlogiston from them. Stahl proposed that metals were made of calx, or ash, and phlogiston, and that once a metal is heated, the phlogiston leaves only the calx within the substance.He was able to make the theory applicable to chemistry as it was one of the first unifying theories in the discipline. Phlogiston provided an explanation of various chemical phenomena and encouraged the chemists of the time to rationally work with the theory to explore more of the subject. This theory was later replaced by Antoine-Laurent Lavoisier’s theory of oxidation. He also propounded a view of fermentation which in some respects resembles that supported by Justus von Liebig a century and half later. Although his theory was replaced, Stahl's theory of phlogiston is seen to be the transition between alchemy and chemistry.

Tonic Motion
As a physician, Stahl worked with patients and focused on the soul, or anima, as well as blood circulation and tonic motion.Anima was a vital force that when working properly would allow the subject to be healthy, however, when malfunction of the anima occurred, so did illness. Tonic motion, to Stahl, involved the contracting and relaxing movements of the body tissue in order to serve the three main purposes. Tonic motion helped explain how animals produce heat and how fevers were caused. In Stahl's 1692 dissertation, De motu tonico vitali Stahl explained his theory of tonic motion and how it was connected to blood flow within a subject, without citing William Harvey's blood flow and circulation theories, which lacked an explanation of irregular blood flow. Also within the dissertation, 'practitioners' were mentioned as users of his theory of tonic motion. Tonic came from torus, or tension. This was appropriate since Stahl's theory of tonic motion was about the tension in the circulatory system. During his work at Halle, Stahl oversaw patients experiencing headaches and nosebleeds. Tonic motion explained these phenomena as blood needed a natural or artificial path to flow when a part of the body is tensed or when an external force, such as an impact, seen by swelling of the area. Menstruation was another phenomena Stahl worked with, finding that bloodletting in an upper portion of the body would relieve bleeding during the period. During the next period, the wound would experience pain and swelling which would only be relieved by an opening in the foot. This procedure was also a treatment for a woman experiencing a lack of menstruation.