Alewives Alosa pseudoharengus are the dominant prey fish in Lake Ontario, and their response to ecological change can alter the structure and function of the Lake Ontario food web. Using stochastic population-based bioenergetic models of Lake Ontario alewives for 1987–1991 and 2001–2005, we evaluated changes to alewife production, consumption, and associated bioenergetic ratios after invasive-induced food web disruption. After the disruption, mean biomass of alewives declined from 28.0 to 14.6 g/m2, production declined from 40.8 to 13.6 g·m−2·year−1, and consumption declined from 342.1 to 137.2 g·m−2·year−1, but bootstrapping of error sources suggested that the changes were not statistically significant. Population-based bioenergetic ratios of production to biomass (P/B ratio), total consumption to biomass (Q/B ratio), and production efficiency did not change. Pathways of energy flow measured as prey-group-specific Q/B ratios changed significantly between the two time periods for invasive predatory cladocerans (from 0.6 to 1.3), Mysis diluviana (from 0.4 to 2.5), and other prey (from 0.8 to 0.1), but the observed decline in the zooplankton Q/B ratio (from 10.6 to 5.5) was not significant. Gross production efficiency did not change; values ranged from 8% to 15%. Age-group mean gross conversion efficiency (GCE) declined with age; GCE ranged from 7.5% to 11.0% for yearlings, was approximately 5% for age-2 alewives, and was less than 2% for age-3 and older alewives. The GCE increased significantly between the time periods for yearling alewives. Our analyses support the hypothesis that after 2003, alewives could not sustain their growth while feeding on zooplankton closer to shore. Modeling of observed spatial variation in diet and alternative occupied temperatures demonstrates the potential for reducing consumption by alewives. Our results suggest that Lake Ontario alewives can exploit spatial heterogeneity in resource patches and thermal habitat to partially mitigate the effects of food web disruption. Fish management implications are discussed.