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This article provides a comparative performance analysis of different acquisition and tracking methods of GPS L1 C/A and GPS L5 signals testing their robustness to the presence of scintillations in the propagation environment. This article compares the different acquisition methods in terms of probabilities of detection/false alarm, peak-to-noise floor ratios for the acquired signal and execution time, assessing the performance loss in the presence of scintillations. Moreover, robust tracking architectures that are optimized to operate in a harsh ionospheric environment have been employed. The performance of the carrier tracking methods, namely, traditional phase-locked loop (PLL) and Kalman filter based-PLL, have been compared in terms of the standard deviation of Doppler estimation, phase error, phase lock indicator (PLI), and phase jitter. The article is based on real global navigation satellite systems (GNSS) signals affected by significant phase and amplitude scintillation effects, collected at the South African Antarctic research base (SANAE IV) and Brazilian Centro de Radioastronomia e Astrofisica Mackenzie (CRAAM) monitoring stations. Performance is assessed exploiting a fully software GNSS receiver, which implements the different architectures. The comparative analysis allows to choose the best setting of the acquisition and tracking parameters, in order to allow the operation of signal acquisition and tracking at a required performance level under scintillation conditions.