The Department of Agriculture, as defined in KRS Chapter 246, is headed by the Commissioner of Agriculture, a Constitutional Officer. The State Board of Agriculture, appointed by the Governor, acts as an advisory body to the elected Commissioner.

The Office of the Commissioner provides leadership and management for the Department. The office assists the Commissioner in promoting and encouraging the organization of agricultural organizations and associations.

The Office for Agricultural Marketing develops and manages programs which promote Kentucky-produced agricultural products, including grading and inspecting specific products and commodities and reporting market news. The divisions that make up this office include the Promotion and Development Division, the Shows and Fairs Division, the Livestock Division, the Plant Division, the Education and Outreach Division, and the Direct Farm Marketing Division. Responsibilities of this office include the research, development, and promotion of new and expanded outlets for Kentucky's agricultural products, agricultural education, agritourism development, livestock, farm safety, and farmland preservation. The Office is also responsible for providing testing services for hay and other forages essential for Kentucky's livestock industries and sponsoring district, state, and national livestock shows and sales.

The Office for Consumer and Environmental Protection directs programs which have a direct bearing on agricultural revenue. The divisions in this office include, the Division of Regulation and Inspection, the Division of Food Distribution, and the Division of Environmental Services. The Office conducts the grain regulation program, certifies all sales made by solid weight or liquid volume, licenses egg wholesalers, and inspects amusement rides operating within the Commonwealth. Duties include the distribution of commodity foods to qualifying institutions and individuals on behalf of the United States Department of Agriculture. This office is responsible for conducting various pest and noxious weed control programs, enforcing federal and state laws and regulations pertaining to the control of pesticide use and application, and liaison between the regulator and those being regulated.

The Office of State Veterinarian protects the livestock industry pursuant to KRS Chapter 257. The primary function of this office is the prevention and eradication of animal disease, and to ensure the health of the state's multi-billion dollar animal agriculture industries. The Office enforces Kentucky's statutes on animal importation and movement, and provides numerous other services to the livestock and poultry industries. The Office of State Veterinarian includes the Division of Regulatory Field Services, the Division of Animal Health Programs, and the Division of Emergency Preparedness and Response.

The Office of Administrative Services deals with the budget preparation and administration, handles legislative tracking duties, interacts with government agencies, provides technology systems infrastructure, oversees purchasing and accounting, and ensures fairness for all Department of Agriculture employees. The Office is compromised of the Division of Human Resources, the Division of Administrative Services, and the Division of Information Technology.

The Office of Communications informs the public on news about Kentucky agriculture and shares stories about the Kentucky farm families and agribusinesses that are responsible for the goods provided.

The Office of Legal Services handles the legal needs of the Department as well as serving as the legislative liaison to members of the Kentucky General Assembly, representing the Department and its employees in administrative hearing and court proceedings, and responding to open records requests from the public.

Senate Bill 3 from the 2021 Regular Session of the General Assembly abolished the Governor's Office of Agriculture Policy and established the Kentucky Office of Agricultural Policy within the Department of Agriculture. The office is comprised of two boards, The Kentucky Agricultural Development Board and the Kentucky Agricultural Finance Corporation, which are staffed by the employees in this Office. The Kentucky Agricultural Development Board employs an Executive Director to carry out the duties of the board, while also serving as the Executive Director of the Kentucky Agricultural Finance Corporation.