The populations of the Japanese macaque (Macaca fuscata), which were vulnerable until the early 20th century, have recently recovered. However, this recovery process has rarely been hailed as a conservation success, because it has triggered serious conflicts between people and the macaques. The key exacerbating causes of the conflicts have been the drastic changes in the interrelations between the people, forests, and macaques, as well as the unprecedented social changes in modern Japan (i.e., nationwide depopulation). The aim of this review was to illustrate the bigger picture of these conflicts, by untangling the key root causes, and presenting the outcomes of previous macaque management efforts, which have rarely been presented to the global scientific community. Although recently acquired knowledge regarding macaque management has the potential to support the development of future solutions for the human-macaque conflicts, inadequate responses to the key causes of the physical and psychological hollowing-out of communities across Japan, should be understood as a limiting factor for conflict resolution. This review demonstrates the significance of seeking a resolution for this problem under a wider framework, in order to restructure community designs to be appropriate for the new era of shrinking communities.