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<i>Background and objectives:</i> High-density lipoprotein cholesterol (HDL-C) is important for improving risk estimates of atherosclerotic cardiovascular disease. We investigated the effect of omnivore and diverse vegetarian diets in connection with exercise on HDL-C. <i>Materials and Methods:</i> Historical data of 9588 biobank participants (4025 exercisers and 5563 non-exercisers) aged 30&#8722;70 years were categorized as omnivores (n = 8589), former vegetarians (n = 544), lacto-ovo vegetarians (n = 417), and strict vegetarians (n = 38). We used multiple linear regression for analyses. <i>Results:</i> HDL-C levels were higher in exercisers compared to non-exercisers. Compared with omnivores, strict vegetarians had decreased levels of HDL-C (<i>&#946;</i> = &#8722;5.705; <i>p</i> = 0.001) followed by lacto-ovo vegetarians (<i>&#946;</i> = &#8722;3.900; <i>p</i> &lt; 0.001) and former vegetarians (<i>&#946;</i> = &#8722;0.329; <i>p</i> = 0.475). The test for trend was significant (<i>p</i> &lt; 0.001). After categorization by exercise modalities, the <i>&#946;</i>-value was &#8722;13.984 for strict vegetarians, &#8722;4.419 for lacto-ovo vegetarians, and &#8722;1.864 for former vegetarians, respectively (<i>p</i> &lt; 0.05). There was an interaction between diet and exercise (<i>p</i> = 0.009). Omnivores who exercised regularly had significantly higher HDL-C, whereas strict vegetarians who exercised regularly had significantly lower HDL-C. <i>Conclusions:</i> In summary, strict vegetarian diets in conjunction with regular exercise might not serve as healthful behaviors to be implemented in everyday life considering the negative impact on HDL-C.