He has been working on problems in signal processing and pattern recognition since 1974, with a primary emphasis on speech processing. He is a former Editor-in-chief of Speech Communication, and has been a member of the IEEE Speech Technical Committee, the IEEE Neural Networks Committee, and the ISCA Advisory Council. He is also a Fellow of the IEEE and of the International Speech Communication Association (ISCA). In 1997, he received the Signal Processing Magazine best paper award. He was the Principal Investigator for the multi-site coalition, funded by the DARPA EARS Novel Approaches project, which was the 2002-5 U.S. government program focusing on long-term progress in speech recognition.
Professor Morgan has over 200 publications, including three books; his most recent book is a text (written jointly with Ben Gold, and more recently its second edition with Dan Ellis) on speech and audio signal processing. He holds a number of patents in speech processing methods, including one that is currently being used in millions of CDMA cell phones. His research interests include the redesign from first principles of the primary signal processing used in speech recognition systems and the use of neural networks for the design of these new features. He is also now working on a wholly unrelated project to find structural and technological means to reduce the political influence of large campaign contributions.

Professor Morgan is also on a number of Boards: the Board of Trustees of ICSI; the Board of Trustees of the Toyota Technological Institute at Chicago; the Speech Communication Editorial Board; and Sensory, Inc.'s Advisory Board.