Ionospheric irregularities can cause detrimental effects on the global navigation satellite system (GNSS) signals, often in the form of rapid fluctuations in both amplitude and phase. Over the low-latitude regions, the equatorial plasma bubble (EPB) frequently arises after sunset, leading to GNSS scintillations since the signals propagate through ionospheric irregularities. The relationship between amplitude ionospheric scintillations (S4 index) on GNSS signals and EPB characteristics is presented. We investigate the geometrical relationship between backscatter echoes associated with the EPB and the multi-constellation and multi-frequency scintillations, specifically, GPS and Galileo constellations with L1/E1 and L5/E5a signals. By analyzing the GNSS scintillations along the GNSS signal paths, the GNSS ionospheric pierce points (IPPs) are mapped with S4 index at different altitudes and projected along the magnetic field line together with the backscatter echoes at the equatorial atmosphere radar (EAR), West Sumatra, Indonesia. Our results are obtained for moderate scintillation cases due to limited data available for this study. The results show the EPB impact ionospheric scintillations. The S4 index on the L5/E5a signal is more susceptible to scintillations than the L1/E1 signal. Moreover, we found a high correlation between EAR backscatter echoes and S4 values on both L1/E1 and L5/E5a at an altitude between 250 and 350 km, indicating that the EPB occurs on the bottomside of the ionosphere.