In May 1987 he split from New Democracy and became an independent MP. He did not participate in the June 1989 election, but after a personal invitation by the new New Democracy chairman, Konstantinos Mitsotakis, he rejoined the party and was elected an MP for Corfu. After a renewed dispute with Mitsotakis, now Prime Minister, over the handling of the Macedonia naming dispute, he resigned from his post and retired from politics in March 1993. During his retirement, Rallis established and cultivated organically-farmed vineyards and olive groves at his family estate on Corfu.