Emotional eating (EE) corresponds to a change in eating behavior in response to distress and results in an increase of food intake (overeating (EOE)) or in food avoidance (undereating (EUE)). EE has been related to temperament (i.e. negative emotionality) and dysregulated stress biomarkers in school-aged children; parenting has been understood to influence this relationship in older children. The aim of the study was to investigate to which extent stress biomarkers and negative emotionality are related to EE and to understand the role of parenting in this relationship. The sample consisted of 271 children aged 2-6 years of the Swiss cohort study SPLASHY. We assessed the child's EE, negative emotionality and parenting by parent based reports. Salivary samples were collected over two days to analyze cortisol and salivary alpha-amylase levels. From the whole sample of children, 1.1% showed EOE and 32.9% EUE. Negative emotionality was related to EOE and EUE (0.13 (CI 0.06, 021), p < 0.001; 0.25 (CI 0.14, 0.35), p < 0.001). There was no relationship between stress biomarkers and EE and parenting had any moderating role (all p > 0.05). Similar to a Danish study, parents reported more often EUE than EOE of their child. Both are related to the temperament. Even though the course of EE has not yet been well documented, we conclude that a certain subgroup of children with difficult temperament could be at-risk for eat and weight regulation problems in later childhood.