The relation between Einstein equivalence principle and a continuous quantum measurement is analyzed in the context of the recently proposed flavor-oscillation clocks, an idea pioneered by Ahluwalia and Burgard (Gen. Rel. Grav.29, 681(E) (1997)). We will calculate the measurement outputs if a flavor-oscillation clock, which is immersed in a gravitational field, is subject to a continuous quantum measurement. Afterwards, resorting to the weak equivalence principle, we obtain the corresponding quantities in a freely falling reference frame. Finally, comparing this last result with the measurement outputs that would appear in a Minkowskian space–time it will be found that they do not coincide, in other words, we have a violation of Einstein equivalence principle. This violation appears in two different forms, namely: (i) the oscillation frequency in a freely falling reference frame does not match with the case predicted by general relativity, a feature previously obtained by Ahluwalia; (ii) the probability distribution of the measurement outputs, obtained by an observer in a freely falling reference frame, does not coincide with the results that would appear in the case of a Minkowskian space–time. Concerning this last difference, the probability distribution differs in two directions. Firstly, the maximum, as function of the energy of the system (that emerges if we calculate first the probability distribution in the original curved manifold and then, resorting to the weak equivalence principle, we find the corresponding expression in a freely falling reference frame) is shifted with respect to the case in which the system is in a Minkowskian space–time. Secondly, the magnitude of this maximum is not equal to the respective quantity predicted by general relativity. In other words, we obtain two new theoretical results that predict a violation of Einstein equivalence principle, and that could be measured.