The Joint City/County/County Meetings are an opportunity for the City, Riley County, and Pottawatomie County Commissioners to discuss issues of mutual interest. The agendas for the meetings are mutually set between the City and the Counties as issues arise. There is typically not a provision for public comments as the intent for the joint meeting is for the Commissioners to have a group discussion amongst themselves and may hear presentations from staff on particular projects or subjects. Agenda items are established at the concurrence of the elected officials through their staff and the host of the meeting which alternates between the City (odd months) and Riley County (even months). These meetings are generally the third Thursday of the month at 4:00 p.m., alternating location between the City and Riley County.

The governing and legislative body of the city is the City Commission, comprised of five commissioners who are elected at-large on a non-partisan basis. The commission determines all matters of policy and approves all city ordinances and resolutions, as well as adopts the annual city budget.

The Manhattan Urban Area Planning Board was created in March 1976, through an interlocal agreement between the Manhattan City Commission and the Riley County Commission, to provide for coordinated planning within a jurisdictional area called the Manhattan Urban Area, which includes the Manhattan city limits and the surrounding urbanizing area

The purpose of the Historic Resources Board is to encourage the preservation, restoration and rehabilitation of historic properties within the City through the designation of Historic sites, structures, and districts, pursuant to the City's Code of Ordinances and Kansas State Statute. The Board also advises the City Commission on matters related to historic preservation and issues Certificates of Appropriateness on locally designated historic properties.

Comprised of seven community members, the HRSB’s primary purpose is to receive and consider questions or proposals which in and of themselves do not constitute formal complaints of unlawful discrimination but are related issues, and recommend non-discrimination, equal opportunity and civil rights policies, procedures, and programs to the governing body (City Commission). Those recommendations should be intended to protect against discrimination; promote the health, safety, and welfare of the citizens of the city; and/or create a welcoming, diverse community.