Gaussian graphical models (GGMs) are exploratory methods that can be applied to construct networks of food intake. Such networks were constructed for meal-structured data, elucidating how foods are consumed in relation to each other at meal level. Meal-specific networks were compared with habitual dietary networks using data from an EPIC-Potsdam sub-cohort study. Three 24-hour dietary recalls were collected cross-sectionally from 815 adults in 2010–2012. Food intake was averaged to obtain the habitual intake. GGMs were applied to four main meals and habitual intakes of 39 food groups to generate meal-specific and habitual dietary networks, respectively. Communities and centrality were detected in the dietary networks to facilitate interpretation. The breakfast network revealed five communities of food groups with other vegetables, sauces, bread, margarine, and sugar & confectionery as central food groups. The lunch and afternoon snacks networks showed higher variability in food consumption and six communities were detected in each of these meal networks. Among the central food groups detected in both of these meal networks were potatoes, red meat, other vegetables, and bread. Two dinner networks were identified with five communities and other vegetables as a central food group. Partial correlations at meals were stronger than on the habitual level. The meal-specific dietary networks were only partly reflected in the habitual dietary network with a decreasing percentage: 64.3% for dinner, 50.0% for breakfast, 36.2% for lunch, and 33.3% for afternoon snack. The method of GGM yielded dietary networks that describe combinations of foods at the respective meals. Analysing food consumption on the habitual level did not exactly reflect meal level intake. Therefore, interpretation of habitual networks should be done carefully. Meal networks can help understand dietary habits, however, GGMs warrant validation in other populations.