Called Johann Ernst "of Arnstadt" so as not to confuse him with Sebastian's second cousin by the same name, this first cousin is remembered chiefly as the unfortunate individual whom Sebastion appointed to fulfill his duties during his extended leave to Lübeck. Earlier, when Sebastian was living in Lüneburg, Johann Ernst had sojourned in nearby Hamburg for six months during which it is possible that he may have introduced Sebastian to the musical circles of that city. When Sebastian left Arnstadt for Mühlhausen, Ernst succeeded him as organist at the Jacobikirche. In 1728 he was appointed organist of the Liebfrauenkirche--a less-than-enthusiastic hire as the Consistory felt compelled to admonish Ernst: "to exercise himself still better in his art, to improve himself as much as possible by due reflection, not to remain always at one level, but to cultivate his skill by diligent correspondence with one and another among experienced musicians."
Johann Ernst was the son of Johann Christoph, Sebastian's uncle, and twin brother of Sebastian's father, Ambrosius. When Ambrosius moved to Eisenach, his twin moved to Arnstadt where the family resided for many years.