In Pacific Northwest prairies and oak woodlands, cessation of anthropogenic burning in the mid-1800s resulted in large-scale degradation and loss of habitat due to tree and shrub encroachment. Widespread invasive species, deep thatch accumulations, and extensive moss cover now limit the ability of native plants to germinate and thrive. These changes in habitat structure and function have contributed to the decline of several plant and animal species. Over the past decade, prescribed fire has been increasingly applied throughout the Willamette Valley-Puget Trough-Georgia Basin Ecoregion and used in conjunction with other techniques (herbicide, seeding native species) to restore native habitat with variable results. This variability likely is a result of differential fire intensity, dictated by fuels, weather and application technique, all of which can be controlled for by altering fire season, fire frequency, pre-fire treatments and fire extent. In order to burn at the spatial and temporal scales necessary for effective habitat restoration, however, prescribed burn programs must overcome several socio-political, programmatic and economic challenges. This requires a collaborative approach to prescribed fire training, implementation and research. Future research on fire season, fire frequency, species-specific responses to fire and effects of fire surrogates on ecosystem structure and functioning will help to refine prescribed fire management for maximum effectiveness in prairie and oak woodland restoration.