He was the second oldest son of the Frankfurt city physicus (Physikus primarius, medical officer) Johann Hartmann Senckenberg (1655–1730) and his second wife Anna Margaretha born Raumburger (1682–1740).
Although Senckenberg was granted a 100 guilders scholarship through the city four years later, his studies were delayed due to the financial situation.
The deeply religious Senckenberg was impressed by the theologian Johann Konrad Dippel and became involved in theological arguments and refused Eucharist.
After he had suffered from mental problems, his older brother Heinrich Christian Senckenberg helped him in 1737 to obtain his doctorate at the Georg August University of Göttingen.
Under the chairmanship of Albrecht von Haller, he dealt in his dissertation with the healing power of the Lily of the valley (De lilii convallium eiusque inprimis Baccae viribus.
After the death of his three wives and his children, he decided to make his entire fortune available in a Foundation pro bono publico patriae.
Senckenberg stated that a "Collegium medicum" comprising Frankfurt Protestant physicians were the heirs of the Foundation's assets, and that four city doctors were to be testament executors.
Two-thirds of the interest on the Foundation's capital was to be used to promote medicine, although initially it was to be used for the entertainment of the Senckenbergische Wohnhaus, which was equipped with a library and a collection.
The Foundation became called Senckenbergische Stiftung and took as seal the coat of arms of the Senckenberg family: a burning bush.
A total of 53 diary volumes and 600 folders with further notes are now in the Frankfurt University Johann Christian Senckenberg Library.
Due to the hard-to-read handwriting (a mixture of Frankfurt German, Latin, Greek, French and English), as well as numerous idiosyncratic abbreviations, reading and transcribing these diaries is very difficult.
Since 2011, Frankfurt University Library has been working on bringing some 13,000 diary pages from the years 1730 to 1742 into a readable form and making them available online as digital copies.