Invasive species can have negative effects on native biodiversity and ecosystem function, and suppression is often required to minimize the effects. However, management actions to suppress invasive species may cause negative, unintended effects on non‐target taxa. Across the United States, lake trout (Salvelinus namaycush) are invasive in many freshwater ecosystems, reducing native fish abundance and diversity through predation and competition. In an integrated pest management approach, lake trout embryos in Yellowstone Lake, Wyoming, are suppressed by depositing lake trout carcasses onto spawning sites; the carcasses reduce dissolved oxygen concentrations as they decay, causing embryo mortality. We conducted a field experiment during one ice‐free season at four sites in Yellowstone Lake to investigate the non‐target effects of carcass treatment on benthic invertebrates, which could have consequences for native fish diets. While overall invertebrate density and biomass did not respond to carcass treatment, Chironomidae midges and Sphaeriidae fingernail clams decreased in abundance. Carcass treatment altered invertebrate community structure based on density, but not biomass. Carcass treatment to suppress invasive fish embryos has spatially localized, non‐target effects on some benthic invertebrate taxa. Given the small spatial extent of carcass treatment within the lake, we conclude it is unlikely that carcass treatment will alter food availability for native fishes.