This study investigated the effects of mastication and hand-thinning treatments in piñon-juniper (PJ) woodlands on ecological processes including fire, and on a wide range of species, particularly vulnerable PJ obligate birds. Treatments drove major, persistent ecological shifts relative to controls. Tree cover and canopy fuels were reduced; concomitantly, down woody surface fuels, forb, and grass cover increased. Treatments exhibited rapid, large, and persistent increases in the frequency, richness, and cover of 20 non-native plant species including cheatgrass. Treatments substantially reduced the occupancy of piñon-juniper specialist and conifer obligate bird species.