Vegetarian diets have gained popularity in sports. However, few data exist on the status of micronutrients and related biomarkers for vegetarian and vegan athletes. The aim of this cross-sectional study was to compare the micronutrient status of omnivorous (OMN, n = 27), lacto-ovo-vegetarian (LOV, n = 26), and vegan (VEG, n = 28) recreational runners. Biomarkers of vitamin B12, folate, vitamin D, and iron were assessed. Additionally, serum levels of calcium, magnesium, and zinc were examined. Lifestyle factors and supplement intake were recorded via questionnaires. About 80% of each group showed vitamin B12 adequacy with higher levels in supplement users. Mean red blood cell folate exceeded the reference range (>340 nmol/L) in all three groups (OMN: 2213 ± 444, LOV: 2236 ± 596, and VEG: 2354 ± 639 nmol/L; not significant, n.s.). Furthermore, vitamin D levels were comparable (OMN: 90.6 ± 32.1, LOV: 76.8 ± 33.7, and VEG: 86.2 ± 39.5 nmol/L; n.s.), and we found low prevalence (<20%) of vitamin D inadequacy in all three groups. Less than 30% of each group had depleted iron stores, however, iron deficiency anemia was not found in any subject. Our findings suggest that a well-planned, health-conscious lacto-ovo-vegetarian and vegan diet, including supplements, can meet the athlete’s requirements of vitamin B12, vitamin D and iron.