In 1999, she again led an Indian delegation to the Pakistan Peace Conference, organised by Pakistan Peace Coalition and visited many places.
In March 2000, she led a women’s Bus of Peace from Delhi to Lahore, comprising women from every walk of life. That same year, as founder chairperson of Women’s Initiative for Peace in South Asia, she hosted two Buses of Peace from Pakistan to Delhil.
Deshpande also helped retired Services officers to form the Indo-Pak Soldiers’ Initiative for Peace in India and its counterpart in Pakistan. She led a delegation of the India chapter of this organisation to Pakistan in 2001.