Ratcliffe's overgenerous trading provoked Smith to complain that they would soon run out of items to trade. By January 1608, only 38 colonists were alive, and Ratcliffe and the Council planned to return to England on Discovery. Ratcliffe was elected president and asked Smith to organise work details and expeditions to trade with Native Americans. Ratcliffe worked with explorer John Smith to remove Edward Wingfield from the presidency because he was hiding food for himself that the colony needed. Ratcliffe had been sick in the first summer of Jamestown, and never recovered to the change of climate.
During the administration of George Percy, Ratcliffe was sent in October 1609 to build a fort at Old Point Comfort, which was named "Algenourne Fort" after one of Percy's ancestors. Ratcliffe was removed in July 1608 and succeeded by Matthew Scrivener.
Many colonists also disagreed with how he handled trade with the natives and how he performed during the food shortages during the summer of 1608. Ratcliffe fell out of favour with many colonists after enlisting men to build a governor's house. He became president of the colony upon the deposition of Edward Maria Wingfield on 10 September 1607. Discovery was the smallest of all three ships it had a crew of only 21 men. Ratcliffe commanded Discovery and became a councillor of the Jamestown Colony. He served as a seaman before going to Virginia, and he may be the Captain Ratcliffe taken prisoner with Sir Henry Cray and Captain Pigott at Mulheim in 1605. In early life, he changed his name to Ratcliffe as an alias.