Dietary habits are influenced by various determinants that may evolve over time. This study aimed to examine, among adolescents in Belgium, trends in the dietary habits between 1990 and 2014 and to determine changes in family and regional disparities related to diet during this time period. In the 1990, 2002 and 2014 cross-sectional “Health Behaviour in School-aged Children” (HBSC) surveys, food consumption was estimated using a short Food Frequency Questionnaire. The Relative Index of Inequality (RII) enabled quantification of the gradients of inequality related to the family structure and to the region for non-daily fruit and vegetable and daily sugar-sweetened beverage (SSB) consumption. Between 1990 and 2014, the prevalence of non-daily fruit consumption increased from 27.7% to 60.6%, whereas the daily SSB consumption decreased from 58.9% to 34.8%. Over time, a downward trend in family disparities ( p = 0.007) was observed for daily fruit consumption (RII: 1.58 (1.33–1.88) to 1.18 (1.13–1.23)). An upward trend in region-related disparities (p < 0.001) for SSB was found (RII: 1.15 (1.07–1.23) to 1.37 (1.28–1.47)). The overall trend of increasing disparities when dietary habits improved and decreasing disparities when dietary habits worsened highlights the need to implement actions that improve overall dietary habits while ensuring that disparities do not increase.