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We study the way that chromatic dispersion affects the visibility and the synchronization on Quantum Key Distribution (QKD) protocols in a widely-used setup based on the use of two fiber-based Mach-Zehnder (MZ) interferometers at transmitter/receiver stations. We identify the necessary conditions for the path length difference between the two arms of the interferometers for achieving the desired visibility given the transmission distance -- where the form of the detector's window can be considered. We also associate the above limitations with the maximum detection rate that can be recorded in our setup, including the quantum non-linearity phenomenon, and to the maximum time window of the detector's gate. Exploiting our results we provide two methods, depending on the clock rate of the setup, to perform chromatic dispersion compensation techniques to the signal for keeping the correct order of the transmitted symbols. At the end, we apply our theoretical outcomes in a more realistic QKD deployment, considering the case of phase-encoding BB84 QKD protocol, which is widely used. Our proposed methods, depending on the transmission distance and on the photon emission rate at transmitter station, can be easily generalized to every fiber-optic QKD protocol, for which the discrimination of each symbol is crucial.