Cobalamin deficiency represents a health issue for vegetarians, especially vegans, if supplements are not consumed. Vitamin B12 serum levels, traditionally used to assess the vitamin B12 status, can be normal under functional deficiency conditions. In this regard, methylmalonic acid (MMA) has proven to be a more specific marker to detect subclinical vitamin B12 deficiency. In this study, we present for the first time the cobalamin status of Spanish vegetarians using both vitamin B12 and MMA markers, and the effects of the plant-based diet and the intake of vitamin B12 supplements. Healthy adults were recruited (n = 103, 52% vegans). Dietary preferences and use of supplements were assessed by questionnaires and serum samples were collected and stored. Vitamin B12 was measured by chemiluminiscence and MMA by liquid chromatography tandem mass spectrometry (LC-MS/MS) using solid phase extraction for sample preparation. Obtained values, median (IQR), were: vitamin B12, 278.9 (160.2) pmol/l and MMA, 140.2 (78.9) nmol/l. No significant differences between lacto-ovo vegetarians and vegans were observed. Considering these two markers, 10% of the participants were mild vitamin B12 deficient. Supplementation (75% of the participants) was associated with higher vitamin B12 (p < 0.001) and lower MMA (p = 0.012). In conclusion, Spanish vegetarians have low risk of vitamin B12 deficiency due to vitamin B12 supplementation and the MMA determination is useful to detect mild deficiency.