Invasive plants can alter the structure and composition of native plant communities, which can affect ecosystem processes and habitat quality for a wide variety of organisms. Habitat alteration due to invasive plants often has negative consequences for native species, however, the strength, directionality, and shape of effects strongly depends on the interaction between the type of habitat change and native species’ traits, such as natural history characteristics. To prioritize conservation of vulnerable species, it is therefore critical to effectively predict native species’ responses to invasive plants, which may be facilitated by a framework based on species’ traits. We studied changes in small mammal populations and communities, and in habitat heterogeneity, across a gradient of cheatgrass cover in a mixed-grass prairie in northeast Wyoming, U.S.A. In addition, we assessed the ability of native species’ traits, such as habitat association, to predict small mammal responses to cheatgrass invasion. Our habitat heterogeneity index decreased with cheatgrass cover. Species richness did not vary with cheatgrass, however, pocket mouse (Perognathus spp.) and harvest mouse ( Reithrodontomys spp.) occupancy tended to decrease and increase, respectively, with cheatgrass cover, suggesting a shift in community composition. Cheatgrass had little effect on occupancy for the remaining species, and deer mouse (Peromyscus maniculatus) abundance increased marginally with cheatgrass. Species’ responses to cheatgrass primarily corresponded with our a priori predictions based on species’ traits. In our species’ traits analysis, the probability of occupancy varied significantly with a species’ habitat association but not with diet or mode of locomotion. When considered within the context of a particular habitat change by an invasive plant, relevant species’ traits may provide a useful framework for predicting species’ responses to invasive plants. A critical next step in understanding this invasive plant-wildlife relationship was to assess why habitat changes by cheatgrass altered small mammal populations and communities, and to quantify changes in fitness, which more reliably indicate habitat quality. We measured perceived risk by nocturnal rodents using a giving-up density foraging experiment in cheatgrass and native habitats. Habitat selection may also reflect perceived risk, thus we assessed deer mouse microhabitat selection in response to cheatgrass, shrub cover, and moonlight at two spatial scales. Finally, we used mark-recapture to quantify deer mouse apparent survival across a cheatgrass gradient. In our foraging experiment, shrubs were more important as protective cover in cheatgrass dominated habitats, suggesting that cheatgrass increased predation risk. Additionally, deer mice significantly avoided cheatgrass and selected shrub cover at two spatial scales, however, selection for cheatgrass and shrubs did not interact. Deer mouse apparent survival varied with a cheatgrass-shrub interaction, corresponding with our foraging experiment results, and providing a rare example of a native plant likely mediating the effects of an invasive plant on wildlife. When results from all three metrics – foraging behavior, habitat selection, and apparent survival – are considered, it is likely that the increased perceived risk in cheatgrass habitats reflected actual risk with negative fitness consequences for small mammals. Our research is timely given the global scope of current and potential future impacts of invasive plants, particularly annual grasses. By linking changes in small mammal perceived risk and fitness due to cheatgrass invasion, we provide a critical next step to gaining a mechanistic understanding of the effects of habitat alteration due to non-native plant invasion.