Non-native plant invasions can have devastating effects on native plant communities; conversely management efforts can have non-target and deleterious impacts on desirable plants. In the arid sagebrush steppe rangelands of the western United States, non-native winter annual species affect forage production and biodiversity. One method proposed to control these species is to suppress the soil seed bank using the pre-emergent herbicide indaziflam. Our goal was to evaluate the efficacy of indaziflam to control non-native annual mustards (Alyssum spp.) and to understand potential non-target effects of management on the diverse mountain sagebrush steppe plant communities within Yellowstone National Park. Six sites were established along an elevation gradient (1615 – 2437m), each with high and low Alyssum spp. infestations. We applied 63g ai ha−1 of indaziflam in late summer of 2018 and evaluated plant community cover in situ for two years after treatment, and emergence of forb species from the soil seed bank ex situ. Indaziflam was highly effective at controlling Alyssum spp. emergence for two years. Richness and Shannon’s diversity of the non-target plant community were significantly lower in sprayed plots than the control, and both decreased along the elevation gradient. These reductions were due to a decrease in perennial forbs and native annual forbs in the sprayed plots; perennial graminoids were not affected. Overall, the above ground and seed bank community composition was negatively impacted by indaziflam, and these effects were strongest for the native annual forbs that rely on annual regeneration from the seed bank. The effects of this herbicide to the non-target community should be evaluated beyond the length of our study time, however we conclude indaziflam should likely be reserved for use in areas that are severely invaded and have seed banks that are comprised of non-desirable species rather than diverse, native mountain sagebrush communities.