A method of monitoring and controlling a freeze drying process in a freeze drying apparatus having walls, shelves and a number of vials or trays positioned on different areas of the shelves and containing product to be freeze dried. One or more vials or trays are selected that are representative of the positions of all of the vials or trays in different areas of the shelves. One or more heat flux sensors are positioned between the selected vials or trays and adjacent portions of the walls and/or shelves. The heat transfer between the selected vials or trays and the adjacent wall or shelf portions is measured during the freezing and drying stages of the freeze drying process.