Howes was elected to the Chapel Hill Town Council in 1975 and served on continuously until 1987. He was elected Mayor of Chapel Hill in 1987, serving two terms until 1991. Howes focused on improving relations between UNC and the larger Chapel Hill community during his tenure as mayor. Under Howes, Chapel Hill constructed a new town hall, library, and expanded city parks and greenspaces. Additional neighborhoods were also annexed to Chapel Hill in 1990, which required attention to community relations. As Mayor of Chapel Hill, Howes also contributed his expertise on regional planning during his tenure on as the Triangle J Council of Governments. North Carolina Governor Jim Hunt appointed Howes as Secretary of the North Carolina Department of Environment and Natural Resources in 1992. Under Howes, the state government established the North Carolina Parks and Recreation Trust Fund, which provides funding for coastal access programs, state parks and local recreational areas. He served as Secretary for five years, from 1992 to 1997. Howes was later awarded the Order of the Long Leaf Pine, North Carolina's highest honor, for his contributions as secretary.
Return to UNC
In 1997, Howes was appointed Special Assistant to the Chancellor James Moeser for Community Affairs at UNC-Chapel Hill. Howes served as the Special Assistant for both Chancellor Moeser and his successor, Holden Thorp, until his retirement from in 2010. Howes oversaw UNC's "town-gown" relations between the university and the larger community as a special assistant to the chancellor. He and David Godschalk, a former Chapel Hill Town Council member and professor emeritus at the UNC Department of City and Regional Planning, co-chaired the 2000 Campus Master Plan project, which oversaw the planned 6 million square foot expansion of the existing UNC Chapel Hill campus. In addition to his positions at UNC, Howes served as the interim general manager of WUNC Radio, the flagshipNational Public Radio member station for the Research Triangle area of North Carolina, from 2001 to 2002, while the station sought a permanent general manager. He was also a member of WUNC's Community Advisory Board. He served as the interim director of the North Carolina Botanical Garden for almost four months in 2015. Jonathan Howes died of complications from heart disease at UNC Hospitals in Chapel Hill on May 31, 2015, at the age of 78. He was survived by his wife of 55 years, Mary Howes; their three children – Anne Anderson, Betsy Howes-Bean and Bo Howes; and eight grandchildren – Margaret, Elizabeth Karen, and David, Benjamin, and Rebecca, and Jonathan, Maxwell, and Matthew.