A balanced diet has the goal of providing adequate amounts of different nutrients to promote and maintain physical and psychological health. Our aim was to study the association between different sociodemographic, socioeconomic and lifestyle factors and low energy or protein intake among the Swiss population. This is a cross-sectional cohort study based on the national nutritional survey “MenuCH”, which is the first representative, detailed assessment of dietary habits in the adult Swiss population conducted in 2014/2015. We compared the mean protein and caloric intake based on two 24 h recall nutritional assessments with current recommendations based on resting metabolic rate calculation and DACH guidelines. A total of 1919 participants with a median age of 46 years and 53% females were included. Overall, 10.9% and 20.2% of participants had an energy and protein intake, respectively, below the dietary reference values. However, a high income (>9000 CHF per month) reduced the risk of low energy intake (OR 0.49 [0.26–0.94],p= 0.032), obesity (OR 6.55 [3.77–11.38],p< 0.01), and living in a household with children (OR 2.1 [1.15–3.85],p= 0.016) was associated with higher risk. Regarding low protein intake, the most important risk factors were an age group of 65–75 years (OR 2.94 [1.57–5.52],p= 0.001) and female gender (OR 1.73 [1.15–2.6],p= 0.008). Regular meat consumption reduced the risk of low protein intake (OR of 0.23 (0.1–0.53),p= 0.001). Within this survey, several socio-economic and lifestyle factors were associated with low energy and protein intake in the healthy Swiss population. A bunderstanding of these factors may help to reduce the risk of malnutrition.