Methods and systems for estimating propellant transfer in an ion propulsion system are disclosed. One example is a method for estimating transfer of a propellant between a first tank and a second tank in an ion propulsion system during a transfer event. The first tank and the second tank are separated by a valve. A flow rate of the propellant through the valve is calculated based on an initial pressure and an initial temperature of each of the first tank and the second tank for a beginning of the transfer event, calculating, based at least in part on the flow rate, a mass of propellant transferred through the latch over a period of time ending at an intermediate time before an end of the transfer event, and determining an intermediate pressure and temperature for each of the first tank and the second tank for the intermediate time.