Originally started in April 1969 employing various forms of pop and rock music that was aimed at a student listenership, WMOT ran a full-time jazz music format between 1982 and 2009, aimed at a somewhat larger, more adult audience. By the late 2000s, WMOT was one of only a handful of U.S. public radio stations employing a jazz format full-time, without filling much of the broadcast day with news and other genres. At various times in the station's history, it has broadcast MTSU football and basketball games as well; WMOT presently broadcasts those athletic contests, partly because of the lack of interest from commercial stations in the immediate Murfreesboro market in doing so.
In 2008, WMOT lost its annual grant from the Corporation for Public Broadcasting (CPB), due to a number of factors. This loss of revenue, along with appropriations cuts by the state of Tennessee, prompted MTSU officials to consider discontinuing the station in early 2009. However, in late 2009, the university decided to instead merge WMOT's operations into a consortium with the other MTSU media (such as WMTS and the student newspaper) titled the Media Convergence Center, with consequent reductions in the station's subsidy, in order to avoid closing it down.
Along with the reorganization, WMOT decided to make radical scheduling changes, notably discontinuing its exclusively jazz format in order to appeal to a wider audience in the Nashville market. In October 2009, WMOT added news and talk programming to the morning and afternoon "drive time" slots between 5 to 9 a.m. and 4 to 6 p.m. from the BBC and Public Radio International. However, after Nashville public radio outlet WPLN-FM discontinued classical music programming during the daytime on weekdays in 2009, WMOT decided in February 2011 to fill the void by replacing jazz with classical between 9 a.m. and 3 p.m., formerly the hours when WPLN broadcast that format, in order to gain listeners seeking that format. WMOT also brought back, after many years' absence, National Public Radio's flagship program, All Things Considered, despite the fact that it duplicates the program's carriage by WPLN (as does the NPR hourly news updates).
The situation among public broadcasters in the Nashville market became more complicated later that year when that WPLN's parent organization, Nashville Public Radio, acquired the Vanderbilt University student-run station WRVU in June, converting it into an all-classical format under the WFCL callsign, while the main WPLN signal became a full-time news-and-talk outlet. As of 2014, however, WMOT has opted to continue the divided format, despite competition from WFCL and WPLN.