Late spring frost is a major challenge to stone and pome fruit production in northern New Mexico. In this study, three cultivars of peach (Prunus persica)—Challenger, China Pearl, and Contender on Nemaguard rootstocks were planted at 4x10ft planting density with three replications in a 30x72ft high tunnel in April 2017, but severe leaf chlorosis appeared later in the season. We kept the better west row and removed the central and east row. In 2018, tissue-cultured GF677 and Rootpac® R were planted in May and budded in August 2018. Trees were trained to open vase system. Thermostat-controlled propane heaters and fans were employed for frost protection. In 2021, we began securing the sidewalls and the doors of the high tunnel and setting up heaters. In 2022 and 2023, the high tunnel system plus heating system was sufficient to protect blooms and fruitlets from late frosts, and yields averaged 15.8 kg/tree in 2022 and 12.3 kg/tree in 2023, respectively. There was no significant difference among cultivars in either year. However, there were significant differences between rootstocks in 2022, with trees on Nemaguard averaging 24.3 kg/tree across cultivars, while trees on GF677 and Rootpac® R averaging 11.2 and 11.8 kg/tree, respectively. The nearly two years older in age for trees on Nemaguard could contribute to this difference in 2022. There was also a reasonable crop in 2024. By the end of 2024, Trees on Nemaguard with 1-2ft new growth were smaller than plants on GF677 and Rootpac® R, with 1.5-4 ft new growth. There were limited replications in this high tunnel study but GF677 and Rootpac® R were more suitable than Nemaguard rootstock for the high pH soil conditions in New Mexico. Cherry had limited fruit set during this study. In 2022 and 2023, we observed deformed flowers without petals and some flowers with blackened pistils. Only handfuls of cherries were harvested in both 2022 and 2023. The high temperatures inside the high tunnel in summer could affect the floral bud initiation/ development. More studies are needed to clarify the deformed flowers. Growers should be cautious with sweet cherry production in high tunnels in northern New Mexico.