The objective of this paper is to investigate the ionosphere scintillation impact on the Galileo E1 and E5 open service (OS) signals through the comparison of carrier to noise ratio, amplitude and phase scintillation indices. These indices are obtained by processing correlator and phase measurement outputs of a customized Galileo software receiver in Matlab on one side, and a Septentrio PolaRxS PRO receiver on the other. The collection of global navigation satellite systems (GNSS) data is performed in an equatorial region in Ascension Islands where scintillation is known to be a common event. Code acquisition and tracking routines are specially tailored to take into account each frequency band’s signal structure, including chip rate, primary/secondary code, and dedicated subcarrier. Considering the pilot channel where no data message is encoded, the phase lock loop (PLL) uses a coherent extended arctangent discriminator to accept a wider carrier phase error. The choice of all these strategies is motivated by the desire to maintain receiver carrier and code phase lock in challenging scintillation conditions. On the Galileo E1 OS frequency band, the locally generated code used as a reference to perform tracking, is comprised of the spreading code multiplied by a special subcarrier, the composite binary offset carrier CBOC(6,1,1/11). Due to the shape of the autocorrelation function of binary offset carrier (BOC) signals in general, ambiguous tracking is a common threat. For that reason, an unambiguous code phase detector is inserted in the delay locked loop (DLL) and a modified version of the two-step CBOC tracking [1] is implemented. E5a and E5b signals are treated like binary phase shift keying (BPSK) signals when separate frequency bands are considered, and so typical BPSK DLL tracking is applied. To harness the superior tracking capability offered by BOC subcarriers, a wideband front-end is needed inside a Galileo receiver to capture the entire tracking capability of Galileo signals. It is expected that Galileo wideband signals exhibit superior tracking permeability during scintillation events.