Using the data obtained from XMM-Newton, we show the gradual evolution of two periodicities of ~4500 s and ~2200 s in the decay phase of the flare observed in a solar analog EK Dra. The longer period evolves firstly for first 14 ks, while the shorter period evolves for next 10 ks in the decay phase. We find that these two periodicities are associated with the magnetoacoustic waves triggered in the flaring region. The flaring loop system shows cooling and thus it is subjected to the change in the scale height and the acoustic cut-off period. This serves to filter the longer period magnetoacoustic waves and enables the propagation of the shorter period waves in the later phase of the flare. We provide the first clues of the dynamic behaviour of EK Dra's corona which affects the propagation of waves and causes their filtering.