It's unknown where Hähnel apprenticed and when he arrived in Saxony. (Several archives referred to Johann Ernst as a "foreigner," suggesting he grew up and likely trained in his native Rheinland-Pfalz or a different region.) In 1718, twenty-one-year-old Johann Hähnel married a daughter of the Dresden court organ builder Andreas Tamitius (1633—1700). He soon began working at the organ workshop of his brother-in-law, Johann Gottfried Tamitius (d. pre-1741). Around 1725, Johann Ernst launched his independent studio in Meissen, 25 km northwest of Dresden. His business proliferated, and in 1741, Hähnel earned the highest title of the court's organ builder, Königl. Poln. und kurfürstl. Sächs. Hof- und Land-Orgelbaumeister (translates as "Royal Polish & electoral Saxon Court and Country organ builder"). Johann Ernst remarried in April 1755 to a woman 32 years younger. Circa 1756, he established a new workshop at Hubertusburg.

Even though Hähnel was primarily active as an organ builder, he made stringed keyboard instruments, such as clavichords. Johann Ernst constructed pantalons, a distinct type of concert dulcimers, for its inventor, Pantaleon Hebenstreit (1668—1750). Hähnel also produced an original kind of clavichords, which he named Cimbal Royal, with longer strings struck centrally. In 1731, a German builder, Gottfried Silbermann (1683—1753), sued Hähnel for infringing his original "Cembal d'amour" design in the Cimbal Royal; Silbermann won, and Johann Ernst paid substantial restitution and had to recall his instruments. (Curiously, just four years earlier, Silbermann himself was brought to court by Pantaleon Hebenstreit for producing unauthorized pantalons. In 1727, Gottfried was banned from making such instruments. Thus, his subsequent 1731 lawsuit could've been a payback, of sorts, for this "Pantalon debacle.")

Even in his lifetime, Hähnel was acknowledged among the most important masters in the region, producing over 50 organs of impeccable quality. Despite this, some sources indicate Johann Ernst struggled and lived on the verge of poverty. Hähnel had three daughters from his two marriages and no male heir; thus, he bequeathed the workshop to his son-in-law, Johann Georg Friedlieb Zöllner (1750—1826). Throughout his career, Johann Ernst Hähnel trained many distinguished organ builders at his workbench, most notably Ferdinand Weber (1715—1784) and Adam Gottfried Oehme (1719—1789), as well as Johann Daniel Ranft (1727—1804), Johann Dietrich (1716—1758), and Johann Ephraim Hübner (1713—1781).