Recovered from his ills, Junghuhn returned to Java in 1855. Highly interested in botany and its practical applications, he (together with J.E. 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. This controversy was conducted in public and in print with open letters to and demands on "Het Natuurkundig Genootschap"; part of this exchange of minds can be followed in "Natuurkundig Tijdschrift voor Nederlandsch Indië" from 1862 onwards. At his direction massive plantation of Chincocina was carried out in Java, making it leading producer of Kina (Chinocina bark). He remained on Java until his death from liver disease in 1864. 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. In Lembang, there is a small monument to his memory in a grassy square named after him planted with some of his favorite trees among which the Cinchona. A minor item of trivia playing into polemical discussions of Junghuhn is his surname, literally translated as "young chicken".