Disclosed is a method and system for freezing a biopharmaceutical fluid which is hold in a disposable container. The method includes the steps of arranging the container on the heat transfer surface area, cooling the heat transfer surface area to cool the bottom surface of the container until freezing and forming a layer of ice or an ice block of biopharmaceutical fluid inside the container; dislodging the ice layer or ice block frozen to the container. The steps of cooling the heat transfer surface area and dislodging the ice layer or ice block are repeated until the container is filled with a matrix of frozen biopharmaceutical fluid and liquid biopharmaceutical fluid, the liquid biopharmaceutical fluid occupying interstitial passages between ice layers or ice blocks of biopharmaceutical fluid. The cooling is then maintained until the freezing of the entire biopharmaceutical fluid held in the container.