A process for automated high-throughput fruit or vegetable calyx removal includes a material handling system, a vision system, and a cutting system. The material handling system is capable of transporting the fruit or vegetable through the automated process. The material handling system may also orient the fruits or vegetables along an axis of the fruit and or align the fruit or vegetables in a desired pattern, orientation, and/or configuration. The vision system identifies the calyx and determines calyx position data and optimal cutting angle for individual fruit. The cutting system uses data received from the vision system to automatically remove the calyx from the fruit or vegetables.