It is shown that quantum fluctuation theorems remain unaffected if measurements of any kind and number of observables are performed during the action of a force protocol. That is, although the backward and forward probabilities entering the fluctuation theorems are both altered by these measurements, their ratio remains unchanged. This observation allows us to describe the measurement of fluxes through interfaces and, in this way, to bridge the gap between the current theory, based on only two measurements performed at the beginning and end of the protocol, and experiments that are based on continuous monitoring.