Amuro was placed under house arrest shortly after the war due to the government's mistrust of Newtypes. While he lived in a luxurious mansion and was officially free to come and go as he pleased, Amuro's house servants were actually government agents assigned to keep track of his movements. Amuro worked as a maintenance worker in the Cheyenne Mobile Suit Academy up until the time of the Gryps Conflict. He suffered from chronic combat fatigue, as commented by Emma Sheen and Beltorchika Irma, likely from his traumatic experience during the One Year War and the sense of guilt over killing Lalah Sune.

During the Gryps War, a pregnant Fraw Bow, with her three adopted children, came to visit Amuro. They managed to re-ignite Amuro's fighting spirit and helped him escape from his government handlers. After joining the Karaba, Amuro became a key figure within the group, leading several crucial missions, including the attack on the Titan's base in Mount Kilimanjaro and the seizing of Federation's Congress Building in Dakar.