Perfluoroalkyl substances (PFAS) are a complex group of anthropogenic compounds with exceptional properties. Due to their high persistence and mobility, they have caused ubiquitous environmental contamination and in part accumulate in the food chain. In the general population, diet is the main source of PFAS exposure, with the important sources fish and meat. As a vegan diet implies the complete exclusion of any animal products, it might be expected that vegans have lower blood levels of PFAS compared to omnivores. Furthermore, lower levels of cholesterol is one of the well-documented nutritional effects in vegans, but cholesterol levels were also found to be associated with higher PFAS levels in epidemiological studies. To examine the relations of internal PFAS levels and the levels of cholesterol in vegans and omnivores, the cross-sectional "Risks and Benefits of a Vegan Diet" (RBVD) study was used involving 36 vegans and 36 omnivores from Berlin/Germany. Nine perfluoroalkyl substances were quantified in plasma using a triple-stage quadrupole mass spectrometer. Lower median plasma concentrations were found in vegans compared to omnivores for perfluorooctane sulfonic acid (PFOS) (2.31 vs. 3.57 ng/ml, respectively; p = 0.02) and for perfluorononanoic acid (PFNA) (<0.25 vs. 0.41 ng/ml, respectively; p < 0.0001). No significant differences of the median concentrations were observed for perfluorooctanoic acid (PFOA) (1.69 vs. 1.44 ng/ml, respectively, p = 0.26) and perfluorohexane sulfonic acid (PFHxS) (1.96 vs. 1.79 ng/ml, respectively; p = 0.70). The strongest correlations with food groups, derived from a food frequency questionnaire, were observed between levels of PFOA and water consumption (in case of the total study population, n = 72), and between levels of PFOS as well as PFNA and the consumption of 'meat and meat products' (in case of the omnivores, n = 36). Levels of Low Density Lipoprotein (LDL) cholesterol were confirmed to be considerably lower in vegans compared to omnivores (86.5 vs. 115.5 mg/dl, respectively; p = 0.001), but no associations between the four main PFAS and LDL cholesterol were observed (all p > 0.05) at the low exposure level of this study. According to the results of our study, a vegan diet may be related to lower PFAS levels in plasma. We highlight the importance of the adjustment of dietary factors like a vegan diet in case of epidemiological studies dealing with the impact of PFAS on the levels of blood lipids.