Ender travelled in Brazil in 1817 in the retinue of the Austrian Archduchess Leopoldine. Leopoldine, bound for Rio to marry Don Pedro, heir to the throne of Portugal and future emperor of Brazil, was accompanied by a formidable scientific mission which included the Austrian and Bavarian zoologists and botanists Natterer, Pohl, Spix and Martius. Ender was selected personally by Prince Metternich to accompany the party as artist. He spent ten and a half months in Brazil, from 14 July 1817 until 1 June 1818, working in Rio and its surroundings and travelling to Sao Paulo with Spix and Martius before recurrent illness curtailed his travels.
A selection of his work was engraved in Pohl's Atlas zur Beschreibung der Reise in Brasilien and in Martius's celebrated Flora Brasiliensis. For his Brazilian work, see R. Wagner, Thomas Ender no Brazil, Graz, 1997.