In 1839, Middendorff became Assistant Professor of Zoology at Kiev University. In the summer of 1840, Baer asked Middendorff to join his second expedition to Novaya Zemlya (the first one took place in 1837). Due to stormy conditions the expedition failed to reach Novaya Zemlya, but Baer and Middendorff explored Russian and Norwegian Lapland, as well as the Barents and White Seas. Middendorff was tasked with crossing on foot the Kola Peninsula and mapping the peninsula from Kola to Kandalaksha while collecting zoological and botanical material. From 1843 to 1845, on behalf of the St Petersburg Academy of Sciences, he travelled to the Taymyr Peninsula and then along the coast of the Sea of Okhotsk and entered the lower Amur River valley (which at this time was Chinese territory). He published his findings in "Reise in den äußersten Norden und Osten Sibiriens" (Travels in the extreme north and east of Siberia) in German (1848–1875), which included an account of the effects of permafrost on the spread of animals and plants. He also wrote "Die Isepiptesen Russlands" (1855), an account of bird migration in Russia, and a monograph on molluscs, "Beiträge zu einer Malacozoologia Rossica" (1847–1849), in which he coined the term radula. In 1870 he visited the Baraba steppe and in 1878 the Fergana Valley. He died at Hellenurme in Livonia, present-day Valga County, Estonia. Middendorff's grasshopper warbler, Cape Middendorff of Novaya Zemlya, Kodiak bear ("Ursus arctos middendorffi"), and Middendorff Bay of the Taymyr Peninsula are named after him.