Invasive Lake Trout Salvelinus namaycush in the Yellowstone Lake ecosystem have been gillnetted since 1995 to suppress the population and allow for recovery of native Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri. Although gillnetting is effective (Lake Trout population growth rate λ ≤ 0.6 during 2012–2022), the effort only targets free-swimming, age-2 and older Lake Trout. We developed a complementary suppression method using organic (soy and wheat) pellets to cause Lake Trout embryo mortality and reduce recruitment from spawning areas. The entire Carrington Island spawning reef (0.5 ha) was aerially treated with 3.56 and 3.00 kg/m² of pellets in 2019 and 2020, respectively. Pellet decomposition caused dissolved oxygen concentrations to decline to lethal levels at 20 cm depth in the substrate, and pellets mostly dissipated from the reef within 12 d. Lake Trout fry trap CPUE was reduced to zero after ice-off each spring after the treatments. Prior to the treatments, 71 fry were captured during 58 trap-nights of effort in 2017–2019. After the treatments, no fry were captured during 273 trap-nights in 2020 and 2021. Lake Trout CPUE in large-mesh gill nets set near Carrington Island in September did not decline during 2017–2021 and fry were again trapped on the reef in spring 2022, suggesting that adults were not deterred from spawning there in the years after the pellet treatments. Complementary methods that increase mortality of prerecruits may allow for a reduction in gill-netting effort and the long-term costs of maintaining Lake Trout population suppression in Yellowstone Lake. Treatment of spawning areas may improve suppression efficiency for Lake Trout and invasive fish populations elsewhere because entire cohorts are targeted while immobile and temporarily concentrated in relatively small areas.