Global Navigation Satellite System (GNSS) signals have become a useful tool to analyze signal‐in‐space performance in the presence of ionospheric perturbations with a view to improve the performance of satellite‐based systems and services. For this purpose, continuous monitoring of the signal tracking capabilities of commercial GNSS receivers is a priority, particularly from regions around the crests of Equatorial Ionization Anomaly (EIA), which experiences some of the worst‐case scenarios attributed to ionospheric effects. Ample investigations are reported in literature on GPS signal fading characteristics, while the same for GLONASS and Galileo are limited from Indian low latitude region. The present study aims to report cases of cycle slips and loss‐of‐lock observed independently at GLONASS L1 CA, L2 CA and Galileo L1 BC and E5a, along with a comparative study of robustness of L1 signal in three different constellations GPS, GLONASS, and Galileo, sharing more‐or‐less common ionospheric volume. Data analyzed in this study was recorded during March 2014, a period of high solar activity, from station Calcutta (22.58°N, 88.38°E geographic; magnetic dip 34.54°), located near the northern crest of EIA. Results of this study reveal GLONASS L2 CA to be most affected signal out of all, during periods of ionospheric scintillations. However, when constellations are compared for a particular frequency (L1), Galileo appears to be the least affected. Results of this study could be significant toward better understanding of scintillation effects on GNSS signals while developing more robust applications, especially for a low latitude station.