He was the fourth (but second surviving) and youngest son of Johann Frederick II, Duke of Saxony and Countess Palatine Elisabeth of Simmern-Sponheim.

For this purpose he accepted an outlawed knight, Wilhelm von Grumbach, with himself, which led finally to the fact that also over his father the anger of the Emperor.

Only one year after his birth was besieged the castle of his father in Gotha by troops of the Elector Augustus of Saxony and finally conquered.

In the Diet of Speyer (1570), the Emperor decided to restore to the three sons of Johann Frederick II his hereditary rights.

During there minority, the lands were under the guardianship of the three Elector Princes: Frederick III of the Palatinate (also his maternal grandfather), Johann George of Brandenburg and Augustus of Saxony; also, they took the regency over Saxe-Coburg-Eisenach.

During his first year of reign, Johann Ernst still live in Marsuhl because Eisenach, the new capital of his country, was inhabited and, only with the establishment of his official residence the citizens began to moved there.

For this, Johann Ernst inherited Saxe-Coburg, and until his own death he governed both countries in a personal union, but maintains, however, his residence in Eisenach.