This understanding of the importance of external missions for the church filled the heart of Yannoulatos. Following his ordination to the diaconate in 1960, Yannoulatos founded the inter-Orthodox mission center “Porefthentes”. The goal of this center was to educate the church in the area of missions, as well as to motivate and send missionaries throughout the world.
    Yannoulatos himself planned on becoming a foreign missionary. Immediately following his ordination to the priesthood on May 24, 1964, he left for East Africa and celebrated his first liturgy in Uganda. Shortly after his arrival, however, the young priest contracted malaria and  returned to Greece. Despite his doctor’s recommendation he not return to Africa, Yannoulatos was not daunted by the setback. He realized more than ever the importance of increasing the missionary awareness in the church and sought new ways to fulfill the Great Commission of Christ. Following the advice of one of his professors, Yannoulatos decided the best way he could influence the church was by making a significant contribution in the academic world. He believed  that if he could not directly work in the mission field, he could still try to pave the way for others to go. He decided to pursue further studies in missiology and the history of religions.
   From 1965-69, Yannoulatos studied the history of religions at the universities in Hamburg and Marburg in West Germany, with an emphasis on “Religious Plurality and the Orthodox Church”. His work focused on the general history of religions, African religions, missiology and ethnology. He traveled to Makerere University in Kampala, Uganda, to conduct field research and collect material for his doctoral thesis, “The Spirit Mbandwa and the Framework of Their Cults: A Research of Aspects of African Religion”. Overall, he desired to establish a basis for the whole  process of a serious study of missions in the Orthodox Church. Through this research, he sought support for his original thesis that it was impossible to truly be Orthodox without having an interest in missions.
   Along with his studies, Yannoulatos actively participated in the worldwide ecumenical  movement. By taking part in the Commission on World Mission and Evangelism (CWME) of the World Council of Churches (WCC), the budding missiologist felt that he could both learn from other Christian traditions, as well as introduce these members to the rich missionary heritage of the Orthodox Church. In 1963, Yannoulatos became the youngest member of the CWME at the Mexico City conference. He has continued to play a pivotal role in this ecumenical setting, and ultimately served as its moderator from 1984-91, the first Orthodox missiologist to hold such a place of leadership.