Disclosed are methods and apparatuses for grease separation during a cooking cycle of a food product in a cooking device. The methods and apparatuses perform grease separation by bifurcating the cooking cycle. In a first portion of the cooking cycle, in which the system is closed to ingress of the atmosphere by creating a water barrier in a collector box to seal a cooking chamber in which the food product is cooking, all cooking fluids exiting the cooking device pass into the water barrier. In a second portion of the cooking cycle, the collector box is emptied and the system is opened to capture all cooking fluids exiting the cooking device in the collector box. During the open portion, a grease/cooking fluid interface is monitored and the captured cooking fluids, containing a high percentage of grease, are pumped out of the collector box.