Krill (Euphausia superba) and salps (Salpa thompsoni) are key macrozooplankton grazers in the Southern Ocean ecosystem. However, due to differing habitat requirements, both species previously exhibited little spatial overlap. With ongoing climate change-induced seawater temperature increase and regional sea ice loss, salps can now extend their spatial distribution into historically krill-dominated areas and increase rapidly due to asexual reproduction when environmental conditions are favorable. Understanding the potential effects on krill is crucial, since krill is a species of exceptional trophic significance in the Southern Ocean food web. Negative impacts on krill could trigger cascading effects on its predators and prey. To address this question, we combined two individual-based models on salps and krill, which describe the whole life cycle of salp individuals and the dynamic energy budget of individual krill. The resulting new model PEKRIS (PErformance of KRIll vs. Salps) simulates a krill population for 100 years under varying chlorophyll-a concentrations in the presence or absence of salps. All of the investigated krill population properties (abundance, mean length, and yearly egg production) were significantly impacted by the presence of salps. On the other hand, salp density was not impacted if krill were present. The medians of krill population properties deviated during variable maximum chlorophyll-a density per year when salps were introduced by − 99.9% (− 234 individuals per 1000 m3) for krill density, − 100% (− 22,062 eggs per 1000 m3) for krill eggs and − 0.9% (− 0.3 mm) for mean length of krill. If both species compete for the same food resource in a closed space, salps seem to inhibit krill populations. Further simulation studies should investigate whether this effect prevails if different phytoplankton sizes and consumption preferences of krill are implemented. Furthermore, direct predation of the two species or consumption of krill fecal pellets by salps could change the impact size of the food competition.