In 1886 he joined the Naval Torpedo Station and War College at Newport, Rhode Island as a chemist, where he discovered the Munroe effect, the basis for explosive shaped charges. From 1892–1989 Munroe was head of the Department of Chemistry and Dean of the Corcoran Scientific School at the Columbian University (renamed George Washington University in 1904). During the same time period, he was also the Dean of the Faculty of Graduate Studies and earned a Ph.D. in 1894 and LL.D in 1912 from the University. In 1919 he became Dean Emeritus of the School of Graduate Studies and Professor Emeritus of Chemistry, roles he kept until he died. He wrote over 100 books on explosives and chemistry, and was appointed in 1900 by the Swedish Academy of Science to nominate the candidate for the Nobel Prize in chemistry. In addition, Munroe served as president of the American Chemical Society in 1898 and as a consultant to the United States Geological Survey and the United States Bureau of Mines.