Jonathan Dickinson was born in 1663 in Jamaica. His father Francis had raised a troop of horse for Oliver Cromwell's Western Design expedition to capture Spanish possessions in the Caribbean, and had taken part in the English seizure of Jamaica in 1655, for which he had been rewarded with two plantations. Jonathan's brother Caleb stayed on the plantations while Jonathan became a merchant in the then chief port city of Jamaica, Port Royal. The earthquake of 1692, which nearly destroyed Port Royal, caused the Dickinson family great financial losses.