Purpose: The risk of inadequate micronutrient intake is a concern of low-climate impact diets. This study analyzes the prevalence of iron deficiency (ID) among adolescents with varying dietary climate impact, with special reference to different types and dietary sources of iron. Methods: Data on dietary intake (n = 3099) and plasma ferritin (n = 1030) were from Riksmaten Adolescents 2016–2017 survey of Swedish girls and boys aged 11–18 years. Dietary climate impact was estimated with life cycle assessment data. Linear and logistic regression models assessed associations between dietary climate impact, intakes of iron and food groups, and ID. Results: Higher total iron and heme, but not non-heme, iron intake, was linearly associated with higher dietary climate impact. Compared to girls, boys had higher climate impact and low prevalence of ID. Girls in the highest climate impact quartile had 56% lower odds of ID (OR 0.44, 95% CI 0.24–0.81) compared to the lowest quartile, whereas no association was found in boys. Lower intake of red meat and heme iron was associated with ID in girls, while higher intake of dairy was associated with ID in boys. Menstruating girls and adolescents born outside of Sweden were identified risk groups for ID. Conclusions: Girls with a more climate-friendly diet and lower intake of red meat/heme iron may be at higher risk of ID compared to girls with higher dietary climate impact. These results highlight the importance of considering risk groups of ID, such as menstruating girls, in the transition to more plant-based diets with lower climate impact.