Young people choose energy-dense, nutrient-poor diets, yet understanding of potential determinants is limited. Associations between food choices, mental wellbeing, health-related quality of life (HRQoL) and family affluence were explored to identify targets for intervention to promote dietary health and wellbeing in young people. Adolescents were recruited via post-primary schools in the UK and surveyed at two time-points when aged 13-14 years and 15-16 years. The questionnaire enquired about mental wellbeing using the Short Warwick-Edinburgh Mental Wellbeing Scale, HRQoL using the KIDSCREEN-10, socio-economic status using the Family Affluence Scale and food choice by Food Frequency Questionnaire (FFQ). With missing and anomalous cases excluded, the sample comprised 1208 cases. Factor analysis on the FFQ indicated five food choice factors: ‘Junk Food’; ‘Meat’; ‘Healthy Protein’; ‘Fruit/Vegetables’; ‘Bread/Dairy’. Multivariate regression analysis indicated that frequent consumption of Junk Food was associated with being male and lower mental wellbeing. Frequent Meat intake was associated with being male and with lower HRQoL. Frequent choice of Bread/Dairy foods was more common among males and associated with higher wellbeing and greater affluence. Those who consumed Fruit/Vegetables frequently were more likely to be female, have higher HRQoL, higher mental wellbeing, and greater family affluence. These direct associations endured between time points. The dietary factors were not mutually exclusive. Those who frequently chose Junk Food were less likely to choose Fruit/Vegetables. Frequent choice of Meat was associated with more frequent choice of Junk Food and Healthy Protein. Intervention to improve dietary and psychological health in young people should target males, those in less affluent households, seek to reduce consumption of ‘junk’ food, and increase fruit and vegetable intake.