Haenke was born in Kreibitz (Chřibská), Bohemia, Austrian Empire (today Czech Republic). In 1789, he went to join Alessandro Malaspina and his expedition, but he missed the boat in Cádiz by two hours after travelling from Vienna by France in the eve of the French Revolution. He took another ship to Argentina which capsized at the mouth of Rio de la Plata. After crossing the Andes he arrived in Santiago de Chile on 2 April 1790 and met the Expedición Malaspina. The journey around the world lasted another three years during which the physician, botanist, chemist, and geographer collected several thousand plants.
Afterwards Haenke returned to South America and visited the continent from 1793 to 1810. Napoleon's continental system embargo of 1806 prevented him from returning to Europe and publishing there; instead he ultimately stayed in South America and married. Haenke, who is seen as one of the great ethnological progenitors of Alexander von Humboldt, introduced modern methods to many scientific areas or further developed existing ones.
Haenke's work in Peru, Bolivia, and Chile finally contributed to the creation of the smallpox vaccine. During his expedition through the Atacama desert, he discovered a method for transforming Chile saltpeter and Potassium chloride into Potassium nitrate. Furthermore, he improved explosives and gun powder, giving his results to the Spanish army.