In 1945, Charles de Gaulle sent him to Kunming to help create Military Mission 5 in charge of gathering intelligence and organizing resistance work against the Japanese inside Indochina. The Japanese capitulation in mid-August 1945 took the French by surprise, however. After failed attempts, Sainteny returned to Hanoi in late August 1945 where he later became commissioner for the French Republic in Tonkin and Northern Annam above the 16th parallel (replacing Pierre Messmer who had been captured by the Vietnamese). Sainteny held that position until December 1947 (except for a long interim from May to November 1946 when he was in France).
Shortly after his arrival in Hanoi in August 1945, he met with representatives of the Democratic Republic of Vietnam (DRV), including Ho Chi Minh and other Vietnamese elite and nationalist leaders, communist and non-communist alike. He understood that Ho Chi Minh and his entourage were open to negotiations and less anti-French than the Vietnamese Nationalist Party or the Dong Minh Hoi. On 6 March 1946, faced with the real possibility of Chinese opposition to the landing of French troops in Haiphong, Sainteny received authorization to sign the Accords of 6 March 1946 with Ho Chi Minh and Vu Hong Khanh. In this light, Stein Tønnesson has argued, Sainteny was perhaps not quite the prescient liberal decolonizer some have thought. In any case, Sainteny escorted Ho Chi Minh to France for the Fontainebleau Conference and entertained him during that long summer of 1946.
In November 1946, Georges Thierry d’Argenlieu sent Sainteny back to Hanoi in an attempt to put pressure on Ho Chi Minh to replace key members of the Vietnamese government with more amenable ones. Sainteny followed those orders leading down a dangerous path to full-scale confrontation. He was wounded when his car struck a mine at the start of hostilities on 19 December 1946, but survived and expressed his expectation that the Viet Minh’s house of cards would come tumbling down at its first serious defeat. While this proved seriously wrong, he continued to remain involved in Vietnamese affairs. In 1946, he received the title of gouverneur des colonies, one which he maintained until his retirement in 1968.
After the signing of the Geneva Accords and the division of Vietnam at the 17th parallel in 1954, Sainteny became general delegate for France in Hanoi to the DRV (not an ambassador). Following a mission to Hanoi, he advocated a rapprochement with the DRV, explaining in a 16 September 1954 report that any effort to play the south against Hanoi would “end in failure and perhaps even a new conflict”. However, General Paul Ely and others convinced Pierre Mendès France of the naïveté of Sainteny’s proposal and the anger this might provoke in Washington. Mendès France felt obligated to make up to the Americans for the French National Assembly’s sinking of the European Defense Community earlier that year. In the end, despite an impressive array of contacts spanning the Cold War divide in Hanoi, Sainteny had to content himself with rather consular affairs of an economic and cultural order. He held his post in Hanoi until 1958. His contacts and knowledge of the DRV later allowed him to play an intermediary role in secret negotiations between Washington and Hanoi during the Richard Nixon presidency. Sainteny wrote two books about his time in Indochina and negotiations with Ho Chi Minh: Histoire d’une paix manquée: Indochine 1945–1947 (1953) and Face à Ho Chi Minh (1970).
. His name change was legally accepted in 1949.