Ellis specialised in the study of corals. He was elected a member of the Royal Society in 1754 and in the following year published An essay towards the Natural History of the Corallines. He was awarded the Copley Medal in 1767. His A Natural History of Many Uncommon and Curious Zoophytes, written with Daniel Solander, was published posthumously in 1776.
Ellis was appointed Royal Agent for West Florida in 1764 and for Dominica in 1770. He imported many seeds and plants into England from America, and corresponded with many botanists, including Carolus Linnaeus. His essay Directions for bringing over seeds and plants, from the East Indies.. (1770) included the first illustration of the Venus Flytrap.