[2][6] One of very few Europeans in this settlement on the Kampot River beneath the Elephant Mountains, he "went native", mastering Cambodian, walking bare-foot and sporting a wide-brimmed hat, as he charted the backlands of Cambodia, recording all that he found of interest.

Pavie became his protégé and was entrusted to lead a five-year expedition to explore the region extending from the Gulf of Siam to the great freshwater lake Tonlé Sap in Cambodia and beyond to the Mekong River.

Pavie was enchanted by his new posting: Conquered and charmed, an impression remains with me: dry fishermen's nets strung up along scaffolding; boats pulled half out of the water onto the strand; rafts crossing noisily over the Nam Khan's rapids into the Mekong; white and gold pagodas roofed with coloured varnished tiles; tall houses built in wood and huts constructed with palm leaves, their roofs covered with thin strips of bamboo; lightly dressed men and women climbing up and down the muddy and steeply rising banks between small gardens and providing an appropriate splash of colour; as a final note, and not too far distant, high mountains, dark green in colour, with tufts of cloud rising from the Nam Khan and dispersing about them.Pavie went on to become consul in 1886 and consul general in 1891.

[6] In 1887, Luang Prabang was sacked by Chinese and T'ai bandits, hoping to liberate the sons of their leader Đèo Văn Trị, held prisoner by the Siamese; Pavie prevented the capture of the ailing local ruler Oun Kham by ferrying him away from the burning city to safety in Bangkok, Siam, thereby winning his gratitude and building his trust in French colonial plans, which were to be one of Pavie's major preoccupations from 1888 onwards.

[2] Pavie subsequently established friendly relations with Deo Van Tri, negotiating the release of his brothers; as a result a protectorate treaty was signed with the French in 1889 making Deo Van Tri Lord of Lai Châu, the main town in the Sip Song Chau Tai alliance located in the Black River region of Tonkin that he controlled.

In 1892, he became resident minister in Bangkok, and played an important role in the gunboat diplomacy of the Franco-Siamese crisis in 1893, which resulted in the establishment of the French protectorate over Laos.

He was accompanied by a team of up to 40 assistants, with a wide range of expertise, from archaeology to entomology, some like diplomat-doctor Pierre Lefèvre-Fontalis and the immunologist Alexandre Yersin becoming famous in their own right.

Pavie made a special effort to ensure that the École also trained indigenous assistants, personally accompanying the first Cambodian entrants to France.