Beyond his cabinet position, Leimena agreed to chair the "Pemuda Indonesia Maluku" (PIM), a pro-Indonesian Ambonese organization formed by Johannes Latuharhary. While both Leimena and Latuharhary were respected, they held little control over PIM's activities. Leimena was based in Jakarta in the early days of the revolution, but moved alongside the rest of Sjahrir's cabinet in 1946 to Yogyakarta as Jakarta was being increasingly controlled by the Dutch. Leimena was an important member of the Indonesian negotiating team in agreements with the Dutch. He was part of the Indonesian delegation to the Linggadjati Agreement of November 1946 and the Renville Agreement of January 1948 (during which, Leimena remarked, the Indonesian side accepted the Dutch terms under American pressure). After the Dutch Operation Kraai, Leimena evaded capture and attended talks in Jakarta with representatives from the federal states of the United States of Indonesia in January 1949. During the Roem–Van Roijen Agreement, Leimena also participated in negotiations, and he further participated in the Dutch–Indonesian Round Table Conference in The Hague, leading Indonesia's military delegation.