Battery cells are provided that can include: a housing defining a chamber having a fluid inlet and outlet; an anode at one side of the housing; a cathode at another side of the housing opposing and spaced apart from the anode a sufficient amount to allow for electrolyte between the anode and cathode; and the other side of the chamber defined by an ion permeable member. Methods for in situ battery electrode analysis are provided and these methods can include: providing a battery cell having an anode and a cathode; exposing the battery cell to an ion beam while the battery cell is operational to form secondary ions; and detecting the secondary ions to analyze the battery.