He received permission to stay at the Cape Colony in October 1806, and began work as a clerk in the Royal Naval Victualling Office.
In 1808 he married Antoinetta Adriana Kirchmann, the daughter of an influential German immigrant businessman, and the couple had 12 children.
A man of unusual proactivity, ambition and business acumen, he fought his way to the top of the Cape commercial scene and went on to establish a variety of important enterprises.
(However one of the junior clerks in his merchant house was a boy named John Molteno, an Anglo-Italian immigrant who went on to wrest self-government for the Cape and become its first Prime Minister.)
Ebden was one of the leaders of the renowned anti-convict movement, together with Cape Town Mayor Hercules Crosse Jarvis and Attorney General William Porter, even chairing it in 1849, when he abdicated his Legislative Council seat in protest.
JB Ebden acquired the nickname "the Storm Petrel" due to his combative and independent nature, as well as his tendency to be found in the centre of agitations.