Methods and systems of harvesting a cell product from a cell culture by culturing cells in a fluid medium until the cells have produced a cell product at a harvest concentration are disclosed. The cells are cultured in a cell culture system including a bioreactor connected to an ATF device. The methods include draining fluid medium from the bioreactor through the outlet and the ATF device until the bioreactor volume reaches a predetermined volume, and the ATF column yields at an ATF outlet a liquid containing cell product and passes fluid medium with a concentration of cell product that is lower than the harvest concentration back into the bioreactor, extracting the liquid containing cell product from the ATF outlet, refilling the bioreactor with sterile phosphate buffered saline or fluid medium without any cell product, and repeating steps until a desired amount of cell product has been removed.