Rapid physical growth and the onset of menstruation during adolescence can increase the risk of iron deficiency (ID) and related adverse effects. However, little is known about the risk of anemia and ID among adolescent girls in Ethiopia. Therefore, we aimed to determine the prevalence of ID, low iron stores, and anemia and characterize selected risk factors in Huruta, Arsi Zone, Oromia Region, Ethiopia. A cross-sectional study was conducted among non-pregnant adolescent girls (15-19 years of age; n = 257). Data on household socio-demographic characteristics, anthropometric measurements, and women's dietary diversity score (WDDS) were collected. Hemoglobin (Hb) and serum ferritin (SF), C-reactive protein (CRP), and α-1-acid-glycoprotein (AGP) concentrations were measured. Diets were predominantly plant-based, with a low consumption of animal source foods, fruits, and dark-green leafy vegetables. Only 4% of the adolescent girls had adequate dietary diversity (WDDS ≥5), and 35% were underweight. The prevalence of anemia (Hb <11 g/dL, 8.7%) and clinical ID (SF <15 µg/L, 8.7%) was low, but 41% had marginal iron stores (SF <50 µg/L). The low prevalence of ID, despite a predominantly plant-based diet is atypical and calls for adapted strategies to address low iron stores in this and other similar settings of Ethiopia.