While the expedition was exploring Oceania, the French Revolutionary Wars had broken out in Europe, and when the ships reached Java Labillardière's scientific collections were seized by the British as spoils of war. Labillardière despaired at the loss of three years' painstaking work, but he had an ally in Joseph Banks, who campaigned for the return of the collections. In 1796 his lobbying succeeded, and he was able to write to William Price at the British Museum:
... his Majesty's Ministers have thought it necessary for the honour of the British nation and for the advancement of Science that the right of the Captors to the Collection should be on this occasion wav'd and that the whole should be returned to M. de Billardiere, in order that he may be able to publish his Observations on Natural History in a complete manner ... By this her Majesty will lose an acquisition to her herbarium, which I very much wish'd to see deposited there, but the national character of Great Britain will certainly gain much credit for holding a conduct towards Science and Scientific men liberal in the highest degree.
Labillardière returned to France with his collections in 1796. In 1800 he published an account of his voyage and was elected to the Académie des sciences. Between 1804 and 1807 he published Novae Hollandiae Plantarum Specimen, a description of the flora of Australia.
His is commemorated by several scientific names, including the genusBillardiera and the species Poa labillardieri of tussock grass.