In this brief report, the interplay between meteorological and geomagnetic activity influences on the low-latitude ionosphere is studied. Specifically, the disruption of the dominant wave-4 longitudinal structure of the equatorial ionization anomaly (EIA) by geomagnetic storms is investigated in connection with a sequence of three coronal mass ejections in July 2004. Observations of in situ electron density from the Challenging Minisatellite Payload (CHAMP) satellite are used to investigate changes in the longitudinal structure of the EIA during the different phases of the geomagnetic storms. The observed electron densities at ∼1200 local time during the initial-main phases of the storms does not indicate significant longitudinal structure of the low-latitude ionosphere. A wave-4 structure of the EIA begins to reappear during the storm recovery phases although it is slightly weaker compared to undisturbed conditions. Although the upward propagating atmospheric tides responsible for generating the wave-4 structure of the EIA are not influenced by the geomagnetic storms, changes in the electric fields, neutral winds, and neutral composition due to the geomagnetic storms serve to disrupt the longitudinal structure of the EIA. The results further indicate that the sampling longitude needs to be accounted for when using satellite observations at a fixed local time for geomagnetic storm studies.