Drylands are increasingly degraded by livestock grazing, mining, recreation, off-road vehicles and wildfire. These disturbances damage biological soil crusts (biocrusts) that stabilize soil, cycle nutrients, and store carbon. Farming biocrust as transplantable “sods” offers a promising restoration approach, but invasive plants colonizing sods risk contaminating restoration areas. Manually removing invasives is labor-intensive and unreliable. To determine the viability of herbicide control of weeds while cultivating biocrust, we tested four herbicide treatments, hand-cutting and untreated controls on biocrust sods seeded with the rapidly invading Oncosiphon pilulifer (stinknet) and, later, native plants. We measured biocrust and stinknet cover, native seedling establishment and treatment costs. Late-successional biocrust (lichens, mosses and dark cyanobacteria) grew best under all herbicide treatments compared to controls. Post-emergent herbicides (aminopyralid and glyphosate) effectively controlled stinknet while allowing later native seedling establishment. Preemergent indaziflam prevented both stinknet and native plant establishment. Preemergent aminopyralid was less effective against stinknet. Post-emergent aminopyralid and preemergent indaziflam were most cost-effective and suitable for promoting or preventing native recruitment, respectively. Herbicide application to biocrust sods represents a significant advancement in making biocrust farming economically viable by reducing manual labor, while providing critical information for combating an emerging invasive species threat.