The Mississippi Seed Improvement Association was organized as the official seed-certifying agency and granted a charter in 1940 as a not-for-profit farmers cooperative.

In 1952, the state legislature passed Senate bill No. 274, which created an official seed-certifying agency for the state of Mississippi for the purpose of certifying seeds, plants and plant parts to ensure their quality, integrity and purity. The bill also authorized a state seed board that was empowered and directed to approve rules and standards set forth by the state seed certifying agency.

In 2002, the Mississippi Seed Improvement Association officially changed its name to the Mississippi Crop Improvement Association and was granted authority to provide certification of additional agricultural products.

The Mississippi Crop Improvement Association office is located on the campus of Mississippi State University. MCIA was housed in the old Depot on the MSU campus until moving to its current office at 773 Stone Boulevard.