Despite El Niño events being one of the main forces shaping the coastal desert vegetation in South America, the impacts of the high precipitation typical of this rare but recurrent climatic event remain understudied. Here we monitored the plant community of a coastal lomas, a seasonal desert ecosystem, during 1998 and 2001 to analyse its changes during the 1997-98 El Niño and the following La Niña events. We measured species abundance and vegetation cover in 31 plots, and recorded climate variables in Lomas de Lachay, Peru. We found a significant positive correlation between precipitation and vegetation cover, density, alpha diversity (species diversity at the plot level), total richness and abundance of several key species but no correlation with gamma diversity (species diversity at the whole loma level). During the El Niño event, the seasonality, typical of the lomas ecosystem, disappeared, as evidenced by both the similarity of species composition and mean vegetation cover values between most sampling campaigns of 1998 and 1999. Moreover, total richness was lower during the El Niño event than during the humid season of 2000 and 2001 resulting from the dominance of only a few species, such as Nicotiana paniculata and Loasa urens. Temporal-spatial changes in the abundance of the dominant species caused the differences between alpha and gamma diversity, especially during 1999. Within that year, mean alpha diversity showed similar values whilst gamma diversity values were different. The reestablishment of the seasonality of most plant community characteristics and a clear difference between species composition of the humid and the dry season occurred two years after the El Niño event, suggesting a resilient community. This study provides one of the few quantifications of the Peruvian lomas' response to the 1997-98 El Niño event and the following La Niña, one of the most extreme climatic events in the last century.