A shortage of funds and deteriorating health forced him to live in poor circumstances.
The herbarium was later sold to Unio Itineraria, a Württemberg Botanical Society which had been organized by botanist Christian Ferdinand Friedrich Hochstetter (1787–1860) and physician Ernst Gottlieb von Steudel (1783–1856).
[2][3][4][5] Ecklon received a travel scholarship from the Danish government and in 1829 he went again to Cape Town where until 1833, together with the German botanist and entomologist, Karl Ludwig Philipp Zeyher (1799–1858), he collected a sizable herbarium, a large part of which was handed over to the University of Copenhagen and the University of Kiel.
From 1833-38, he lived in Hamburg and began the publication of descriptions of South African plants in Enumeratio Plantarum Africae Australis Extratropicae, a descriptive catalogue of South African plants in three parts which appeared (1835–37).
The genus Ecklonia (a genus of kelp (brown algae) belonging to the family Lessoniaceae[9]), including Ecklon's kelp (Ecklonia biruncinata or E. radiata), as well as Ecklon's Purple Iceplant (Delosperma ecklonis 'Bright Eyes') and Ecklon's Everlasting (Helichrysum ecklonis) were named in his honour.