Background Dietary guidelines in France give quantitative recommendations for intake of meat, fish and dairy products whereas consumers are increasingly concerned by the environmental impacts associated with the production of these foods. This potentially leads to consumer dilemmas when purchasing food products. The present study aimed at investigating the sociodemographic profiles of individuals reporting health and environmental dilemmas when purchasing meat, fish and dairy products, and comparing diet quality of individuals with and without dilemma. Methods A total of 22,936 adult participants in the NutriNet-Santé cohort were included in this cross-sectional analysis. Participants completed a questionnaire assessing motives when purchasing meat, fish and dairy products, including health and environmental determinants. Environmental vs. health dilemmas were assessed using implicit and explicit methods. Sociodemographic data as well as dietary intake using repeated 24 h–records were collected. The association between sociodemographic characteristics and presence of dilemma was assessed using logistic regression models and between dilemma and intake of these products, adherence to food group guidelines, or overall dietary quality, using covariance analysis. Results Among participants, 13% were torn between buying meat for health reasons and to avoid buying it for environmental reasons, 12% in the case of fish and 5% in the case of dairy products. Older participants, women and low income individuals were more likely to report dilemmas. Participants reporting dilemmas for meat and dairy products consumed less of these foods (P < 0.05 and P < 0.0001, respectively) and had a better dietary quality overall (both P < 0.0001). In addition, participants with meat dilemma showed a better adherence to meat/fish/eggs guidelines (P < 0.001). Conclusions Individuals reporting dilemmas concerning animal products had specific sociodemographic characteristics and showed higher diet quality overall compared with those having no dilemma. Our data suggest that having environmental concerns is not contradictory with adherence to nutritional guidelines.