The departure of his father Johann Georg Heine to the Netherlands in 1828 forced the son to return to Würzburg, where—together with his cousin Bernhard—he took over the management of the Karolinen-Institut for one year.
As he came down with typhoid fever himself he had to return to Bavaria and worked as a physician in Homburg on the Main and in Würzburg, before he applied for the post of district doctor in Waldmohr in the Palatinate.
Heine's next upward step in his career was the appointment as "Kreis- und Medizinalrat der Pfalz", a position which put him in charge of overseeing the health system of this administrative region.
When Johann Georg Heine left Würzburg and his family in 1829 to settle in the Netherlands it must have been shocking for his son Joseph.
When Johann Georg wanted him to take over a hospital in Brussels he rejected the offer and rather completed his medical education in other European cities.
In a publication four years later, Joseph Heine harshly criticized his father for leaving his family and for trying unscholarly methods of medical treatment, but also praised his merits as an outstanding orthopedist.
After Karl's death Heine was good friends with the elder brother Joseph Anselm Feuerbach, who taught archeology in Freiburg.
Joseph Heine soon recognized the artistic talent of his friend's son Anselm Feuerbach and tried to encourage and support him.