ISDA provides oversight on the dairy and egg industries within Idaho. This oversight helps to ensure safe, wholesome milk, milk products, shell egg and poultry products for consumers.

The programs encompass sanitary inspections of dairy farms, bulk milk haulers, processors, manufacturing and processing equipment, warehouses, stores and other businesses where milk and dairy products are manufactured, stored, sold or offered for sale. Other duties include inspection of establishments where shell eggs are packaged, stored or offered for sale. ISDA is also responsible for the protection of surface and groundwater from dairy farm waste, which is accomplished through routine inspections and testing of dairy farm waste handling and containment facilities, land application sites, and review and approval of new or modified systems.

In addition to state enforcement requirements, ISDA works in conjunction with several federal agencies through cooperative agreements or memoranda of agreement to protect the environment and ensure safe food products. Laws and rules require dairy farms to develop nutrient management plans (NMPs) on all licensed dairy farms. These plans also aid in the appropriate applications of nutrients to cropland. A certification process has been implemented to assist in the development of these plans. The department uses ground truthing plans to verify information. ISDA is also responsible with enforcement of the Agriculture Odor Management Act, Title 25, Chapter 38, Idaho Code, as it relates to Idaho dairy farms. Dairy farms that emit odors in excess of those odors normally associated with agriculture in Idaho would be cited by ISDA thereby requiring the facility to develop an Odor Management Plan to reduce odors. ISDA works in conjunction with the University of Idaho and the industry to find economically viable and effective means to minimize offensive odors on dairy farms.