The popularity of oats (Avena sativa) continues to increase in the cereal market due to their health benefits. The recent domestication of Avena magna, a Moroccan oat, presents an opportunity to enhance these benefits due to their higher nutritional composition. As the impact of microclimates on A. magna grain composition has not been explored, this study evaluates twelve A. magna ssp. domestica lines across three Moroccan locations, providing new data into microclimate effects on key grain characteristics. Significant variability is observed among lines and sites for nutrients, with mean protein, fat, and dietary fiber contents at 23.1%, 8.38%, and 7.23%, respectively. High protein levels, reaching 27.1% in Alnif and 26.5% in El Kbab, surpass the ‘Avery’ control (21.7% and 24.2%) in these environments. Groats from Bouchane exhibited elevated fat and fiber contents (10.2% and 9.94%) compared to the control (8.83% and 7.36%). While β-glucan levels remain consistent at 2.53%, a negative correlation between protein content, fat, and starch was observed. A. magna lines exhibited higher levels of iron (7.50 × 10−3 g/100 g DM) and zinc (3.40 × 10−3 g/100 g DM) compared to other cereals. Environmental conditions significantly influence grain quality, with El Kbab yielding higher protein and ash contents, as well as Bouchane having increased fat, fiber, and starch. Stability analysis indicates that fat content was more influenced by the environment, while 25% of protein variability is influenced by genetics. Lines AT3, AT5, AT6, AT13, and AT15 consistently exceeds both the mean for protein and fiber across all sites, emphasizing their potential nutritional value. This study highlights the potential of A. magna ssp. domestica to address nutritional insecurity, particularly for protein, iron, and zinc in domestic settings.