Junghuhn fled by taking service in the Prussian army as a surgeon but was discovered and sentenced to ten years in prison.

Among his works is an important description and natural history in many volumes of the volcanoes of Java, Bijdragen tot de geschiedenis der vulkanen in den Indischen Archipel (1843).

In 1849, ill health forced his return to the Netherlands, where he married Johanna Louisa Frederika Koch on 23 January 1850, and had a son.

The work was controversial, advocating socialism in the colonies and fiercely criticizing Christian and Islamic proselytization of the Javanese people.

The work was banned in Austria and parts of Germany for its "denigrations and vilifications of Christianity", but was a strong seller in the Netherlands where it was first published pseudonymously.

de Vrij of Bandung) became embroiled in a bitter and extended controversy with Johannes Elias Teijsmann, hortulanus of 's Lands Plantentuin at Buitenzorg (now Bogor) and J.C. Hasskarl about the effectiveness of Cinchona species in the treatment of malaria.

On his deathbed in his house near Lembang on the slopes of the volcano Tangkuban Perahu just north of Bandung, Java, Junghuhn asked the doctor to open the windows, so he could say goodbye to the mountains that he loved.

A minor item of trivia playing into polemical discussions of Junghuhn is his surname, literally translated as "young chicken".