Ecological restoration projects have been initiated world-wide with the goal of recovering damaged or degraded ecological systems, increasing the resilience of biodiversity, and providing ecosystem services. Assessment of such projects is essential for improving their implementation and justifying their costs, but comprehensive monitoring and evaluation have rarely been incorporated into projects. We developed a cost-effective monitoring program for lands managed by five Native American tribes in northeastern Washington and adjacent Idaho. Key ecological objectives of restoration are that the restored area (1) has an assemblage of species characteristic of a reference ecosystem that provides appropriate community structure, and (2) consists largely of indigenous species. We established 24 reference points representing the best extant representatives of 8 habitat types, and 83 sampling points on 39 management units where restoration was initiated. Composition and structure of vegetation, and composition and relative abundance of small mammals, birds, and larval amphibians were monitored over 3 years for reference points and at 5-year intervals on restoration sites. Similarity indices that incorporate relative abundance (Chao-Jaccard) were calculated to compare managed lands to the reference for each habitat. Non-metric multidimensional scaling was used to visualize the relationships of restoration to reference sites for each habitat type. Small-mammals appear to be appropriate indicators of change for habitats such as shrub-steppe where there are clear linkages with herbaceous vegetation, and for structurally simple habitats.