After having begun his studies in medicine, Abeel converted and was ordained a minister. He graduated from New Brunswick Theological Seminary in 1826, and was ordained to the ministry that same year. He served as a pastor of his church until the winter 1828, when he went to St. John's, Antigua and Barbuda to recover his health. He was appointed the chaplain of the Seaman's Friend Society. In 1829, he left New York to serve as a missionary. He arrived in Canton, China in 1830, later evangelizing in Java, Malacca, Siam, and Singapore. In 1833, he relocated to Europe, where he visited England, Switzerland, France, Germany, and the Netherlands through 1834.
In 1835, he returned to the United States to recruit additional missionaries from his church to work overseas. He remained in that capacity through 1838, to return to active missionary duty. In 1839, he visited Maritime Southeast Asia, and later established a mission in Xiamen in 1842. In Xiamen, Abeel met with Chinese official and scholar Xu Jiyu, who helped obtain information on conditions in the West. Xu later used this information to compile an influential work on geography.