She was then appointed associate professor in 1981, and professor in 1986. She was appointed assistant research biophysicist in the Biophysics Research Division in 1978, and was promoted to associate research biophysicist in 1981, research scientist in 1988, and research professor in 2001. Dr. Matthews was appointed the G. Robert Greenberg Distinguished University Professor of Biological Chemistry in 1995, and in 2002 she was appointed professor in the Department of Chemistry, and research professor and one of six charter faculty in the Life Sciences Institute. She retired from active faculty status in 2007 and was named the G. Robert Greenberg Distinguished University Professor Emerita of Biological Chemistry, Professor Emerita of Chemistry, and Research Professor Emerita.

Professor Matthews is internationally recognized for her research on folate and vitamin B12 metabolism. She and her colleagues identified the gene for methylenetetrahydrofolate reductase (MTHFR), one of the enzymes involved in managing blood homocysteine levels that are of biomedical importance in cardiovascular disease, strokes, and birth defects. Professor Matthews received the University's Distinguished Faculty Achievement Award in 1996 and was the Henry Russel Lecturer in 2003. She has been elected to the National Academy of Sciences (2002), the Institute of Medicine (2004), and the American Academy of Arts & Sciences (2005).