Knowledge about ecological interactions between species is of paramount importance in ecology and ecosystem-based fisheries management. To understand species interactions, studies of feeding habits are required. In the Baltic Sea, there is good knowledge of the diet of cod, but little is known about the diet of flounder, the second most abundant demersal fish in the region. In this study, we investigated the diets of cod and flounder for the first time using stomach content data collected simultaneously in 2015-2017 over a large offshore area of the southern Baltic Sea. The diet of flounder was relatively constant between sizes and seasons and was dominated by benthos, with a high proportion in weight of the benthic isopod Saduria entomon. The diet of cod differed between seasons and showed an ontogenetic shift with a relative decrease of benthic prey and an increase of fish prey with size. Historic diet data of cod were used to explore cod diet changes over time, revealing a shift from a specialized to generalist feeding mode paralleled by a large relative decline in benthic prey, especially S. entomon. Flounder populations have increased in the past 2 decades in the study area, and therefore we hypothesized that flounder have deprived cod of important benthic resources through competition. This competition could be exacerbated by the low benthic prey productivity due to increased hypoxia, which could contribute to explaining the current poor status of the Eastern Baltic cod. The results of this study point to the importance of including flounder in multispecies end ecosystem models.