Food choices that shape human diets and health are influenced by various socio-economic factors. Vietnam struggles to meet many nutrition targets where links between food choice and diet have not been widely explored. This study assesses the food choice motives, based on a 28-item food choice questionnaire (FCQ), and the diet quality of 603 adults in three sites (urban, peri-urban, and rural) in northern Vietnam. We assess diet quality using the Diet Quality Index–Vietnam (DQI-V) which consists of variety, adequacy, moderation, and balance components. Using factor analysis, we grouped FCQ items into five factors: health focus, sensory appeal, mood ethics, convenience, and familiarity. The structural equation modeling indicates that food choice motives significantly impact the DQI-V and its components but in different directions. The results show that sensory appeal has a positive association with the overall DQI-V score, while having a negative impact on the variety component. Findings present a potential trade-off issue for interventions and policies related to food products. Nutrition knowledge is positively associated with all elements of diet quality across all three study sites. Vietnamese agrobiodiversity could be better utilized to increase dietary diversity. Differentiated policies are necessary to address the poor dietary diversity and adequacy in northern Vietnam.