Success of stream restoration can be difficult to define because many interacting abiotic and biotic factors across spatio‐temporal scales can have measurable effects. Consequently, failure in habitat restoration to achieve targeted biological goals may reflect interactions of habitat restoration with unaccounted risks that have yet to be addressed on the landscape. This is particularly true within invaded landscapes, where habitat restoration can benefit non‐native competitors as much as the native fishes for which restoration is designed. We tested for interacting effects of a reach scale habitat restoration effort and non‐native trout competition on habitat use by a brook trout (Salvelinus fontinalis) metapopulation within a productive main stem corridor of the Shavers Fork watershed, West Virginia. We used a joint species occupancy model within a BACI sampling design to show that brook trout occupancy of main stem habitat was highest post‐restoration within restored sampling reaches, but this benefit to native brook trout was conditional on brown trout (Salmo trutta) not being present within the main stem habitat. Collectively these results indicate that habitat restoration was only beneficial for native brook trout when non‐native trout were absent from the restored sampling area. Proactive approaches to restoration will be integral for supporting resilient ecosystems in response to future anthropogenic threats (e.g. climate change), and we have shown that such actions will only be successful if non‐native competitors do not also benefit from the restoration actions.