Plant-based diets usually contain more nutrient-dense foods such as vegetables, legumes, whole grains, and fruits than a standard Western diet. Yet, the amount and especially the bioavailability of several nutrients, such as trace elements, is supposed to be lower in comparison to diets with consumption of animal-derived foods. Based on this, the Nutritional Evaluation (NuEva) study (172 participants) was initiated to compare the trace element status of omnivores, flexitarians, vegetarians, and vegans. Serum selenium, zinc, and copper concentrations and biomarkers were evaluated at baseline and during a 12-month intervention with energy- and nutrient-optimized menu plans. The implementation of optimized menu plans did not substantially influence the status of trace elements. At baseline, serum selenium biomarkers were lower in vegetarians and vegans compared to omnivores and flexitarians. The zinc intake of vegetarians and vegans was significantly lower compared to omnivores, whereas the Phytate Diet Score was increased. Accordingly, total serum zinc concentrations were reduced in vegans which was, however, only significant in women and was further supported by the analysis of free zinc. Regarding copper status, no differences were observed for total serum copper. Overall, we identified selenium and zinc as critical nutrients especially when maintaining a vegan diet.