Cooley was born in Maryland, but little else is known about his life prior to 1813, when he arrived in East Florida, a province of Spanish Florida, as part of a military expedition. He established himself as a farmer in the northern part of the province before moving south, where he traded with local Indians and continued to farm. During the period in which the region was transferred from Spanish to U.S. governance, he sided with natives in a land dispute against a merchant who had received a large grant from the King of Spain and was evicting the Indians from their lands. Unhappy with the actions of the Spanish, he moved to the New River area in 1826 to get as far as possible from the Spanish influence.