In 1693, determined to devote himself to foreign missionary work, he received permission from the general of his order to travel to the West Indies, then under French domination.

In 1696 he travelled to Guadeloupe, and was appointed procurator-general of all the Dominican convents in the Antilles (Procureur syndic des îles d'Amérique) upon his return to Martinique.

In his account for the year 1698, Labat included his impressions regarding the slaves of Martinique: "The dance is their favourite passion.

However, French scholar Suzanne C. Toczyski reveals a significant tension between, on the one hand, the missionary's infamous acceptance and promotion of slaves as a property to be used (and abused), and, on the other, his appreciation of the slaves as a potential source of knowledge and, more significantly, as others to know, as representatives of a culture of interest from Labat's protoanthropological perspective.

He spent several years in Italy and attended a meeting of the order at Bologna, presenting to the general a report of his work.

The genus of the tropical fruit tree family Sapotaceae Labatia, first described in 1788, was named after Labat.