using multimeter may be we cannot measure internal resistance of MFCs, you have to do polarization (polarization slope methode) or EIS measurement can help you.
I can suggest a very simple method to measure the internal resistance of any real voltage source. To implement it, you need a load resistor R and, of course, a digital (perfect, high resistive) multimeter. Here is the procedure.
First, measure the output voltage E without load (open circuit) by connecting the voltmeter; this will be the electromotive voltage (emf). Then, connect the resistor and measure the voltage drop V across it. Finally, calculate the internal resistance from the voltage divider equation: V/E = R/(R + Rin).
You want to perform a polarization curve, where you will start with the load between the anode and cathode at a very high resistance (closed circuit) and slowly decrease the resistance until there is no resistance (open circuit). At each point, you want to measure the cell voltage (voltage between anode and cathode), and also the anode and cathode voltages against a reference electrode (if possible). Then, you can plot the power density (y-axis) against the current density (x-axis) over the range of resistances. The power density will be at a maximum when the external resistor is equivalent to the internal cell resistance.