Climate change and its impact on agricultural crops is driving the expansion of cropping systems to plants better adapted to rising temperatures, prolonged periods of drought, poor soils, and high salinity. One such crop is quinoa, Chenopodium quinoa Willd (Caryophyllales: Amaranthaceae), a traditionally Andean grain that has been recently adopted in dry, high-elevation regions of Colorado, Idaho, and Washington. However, in 2021, a stem-boring fly, Amauromyza karli Hendel (Diptera: Agromyzidae), was reported in quinoa grown in Colorado’s San Luis Valley and abruptly halted expansion of this climate-resilient crop. This new agromyzid pest has caused complete yield loss in some instances and contributed to substantial declines in quinoa acreage from 3,000 acres in 2021 to 900 acres in 2022. Distinguishing morphological features of A. karli adults include a yellow head, light yellow halteres, a dark brown body, and a dark brown femur and tibia that are yellow near the tips. Larvae feed within quinoa stems and destroy the pith, which disrupts nutrient transport and causes death or significant declines in yield and quality. Here, we summarize the impact of A. karli on quinoa, and discuss life history and management for other agromyzid species that can inform management of A. karli. Research focused on effective integrated management tactics including use of biological control, host plant resistance, and systemic insecticides is urgently needed to suppress this pest.