This article examines the relationship between transnational and intergovernmental organizations in the formation of the international nuclear order in the 1950s. It focuses on three major events in September 1958: the second United Nations (UN) International Conference on the Peaceful Uses of Atomic Energy in Geneva, the third Pugwash Conference on Science and World Affairs (held in Tyrol), and the second General Conference of the International Atomic Energy Agency (IAEA) in Vienna. The three nuclear conferences of 1958, linked closely in time and location, were shaped by interplays of science and politics at a unique moment in nuclear history. The analysis here sheds light on the organizational and institutional beginnings of the Cold War nuclear order and the evolving distinction between transnational and intergovernmental organizations that shaped it. The article shows that competitive dynamics affected relations between the IAEA and the Pugwash organization and between the IAEA and other organizations of the UN.