In 1938, Isogai was transferred to Manchukuo as Chief of Staff of the Kwantung Army shortly before the disastrous Nomonhan Incident.

He was appointed Governor-General of Japanese-occupied Hong Kong on February 20, 1942, at the recommendation of Prime Minister Hideki Tōjō, his former superior officer while serving with the Kwantung Army.

Although Isogai arrived after the worst excesses committed by Japanese troops against civilians during the conquest of Hong Kong, and Isogai's troops (for the most part) were more disciplined than most Japanese forces in mainland China, Hongkongers suffered much deprivation from food shortages.

Public transportation and utilities unavoidably failed, due to shortage of fuel and American air raids killed thousands, leaving more homeless.

Also, Isogai was responsible for the addition of Japanese elements of architecture on the facade of the Hong Kong Government House.