He was educated in southern India, at a school run by Christoph Samuel John and later became a student of Carl Peter Thunberg.
Lebeck was born in Sri Lanka to a Dutch government servant named Abraham Evert de Lebecq (1746–1777).
In 1795 he received a testamur from Uppsala University where he was registered under the name Henricus Julius Lebeck Ceylonensis.
John, Johan Peter Rottler and Johann Gottfried Klein and received a diploma from Berlin's Naturforschende Freunde.
He visited Sri Lanka and then went to Batavia in 1798 where he worked as a mint-master for the Dutch East India Company.