In 1861 Munzinger joined Theodor von Heuglin in an attempt to explore central Africa, but separated from him in November, proceeding along the Gash and Atbara to Khartoum.
There he succeeded von Heuglin as leader of the expedition, and travelled in 1862 to Kordofan, but failed to reach Darfur and Wadai.
[4] He then left the French and entered the service of the Egyptian government of Khedive Ismail, serving as governor of the Keren region and Massawa (modern-day Eritrea).
[3] During the Egyptian-Ethiopian War, Munzinger was selected to command a small expedition intended to open up communication with Menelik II, king of Shewa, a potential ally of Egypt.
[5][6] Munzinger published the following works: He wrote numerous geographical papers, and a memoir on the northern highlands of modern-day Ethiopia and Eritrea for the Zeitschrift für allgemeine Erdkunde, new series, volume 3.