Yellowstone Lake is the site of actions to suppress invasive Lake Trout Salvelinus namaycush and restore native Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri and natural ecosystem function. Although gill netting is effective (Lake Trout λ ≤ 0.6 from 2012 through 2018), the effort costs more than US$2 million annually and only targets Lake Trout age 2 and older. To increase suppression efficiency, we developed an alternative method using organic (soy and wheat) pellets to increase mortality of Lake Trout embryos on spawning sites. Decomposition of pellets during two in situ experiments caused dissolved oxygen (DO) concentrations to temporarily decline to lethal levels (<3.4 mg/L) within days of application. Embryo mortalities during the first exposure period (days 1–6 following application) were high at all treatment levels (1.75–28.0 kg/m²) at the substrate surface and within interstices 20 cm below the surface, varying from 97 ± 1.8% (mean ± SE) to 100 ± 0.0%, but may have been enhanced by a handling effect (exposure to sunlight). Embryo mortalities during the second exposure period (days 11–22) were highest 20 cm below the surface, varying from 78 ± 9.7% to 100 ± 0.0%. Almost all (98 ± 3.1%) Lake Trout embryos died after exposure to DO < 3.4 mg/L for >200 h during the second period. Pellets caused lethal DO for several weeks below the substrate surface, despite largely dissolving and dissipating from the surface of treated areas by day 39. Broad-scale application of pellets at 1.75 kg/m² following the spawning period in autumn may reduce Lake Trout recruitment and enhance population suppression because the area of 14 verified spawning sites is only 11.4 ha (0.03% of lake surface area). Pellet application may be useful in other similar systems as part of an integrated pest management approach targeting multiple life stages of invasive freshwater fish.