The generation and development of ionospheric irregularities is an important topic of study in space weather, mainly because of their adverse effects on navigation and positioning systems, as well as in trans-ionospheric communications. To improve our prediction capabilities, it is necessary to better understand their variabilities during different geomagnetic conditions. The purpose of this research is to analyse the occurrence characteristics of ionospheric irregularities over South America during geomagnetic storms. Using data from six ionosondes and GPS stations in Brazil and Perú, observations from the JULIA radar and Swarm in situ electron density measurements, we examined the presence of irregularities during three intense storms (October 12, 2016, October 7, 2015 and August 25, 2018). Our data show that during the geomagnetic storms that occurred in October 2016 and October 2015, in the Brazilian region, the generation of ionospheric irregularities was usually inhibited during the storm recovery phase. During the main phase, spread-F was generated over the stations located close to the northern crest of the EIA, and it was inhibited over Cachoeira Paulista, a station near the southern crest. During the August 2018 storm, local winter, the geomagnetic activity may have helped generate the irregularities in all the stations analysed regardless of the phase of the storm. We suggest that the generation (inhibition) of irregularities is related to the effect of eastward (westward) storm time electric fields—disturbance dynamo electric fields and prompt penetration electric fields—that created favourable (unfavourable) conditions for the generation of irregularities by uplifting (lowering) the F region.