Food habits vary across ethnic groups and geographical regions. However, validated dietary assessment tools accounting for such diversity remain limited. A semi-quantitative food frequency questionnaire (FFQ) was developed and validated to assess the habitual food intake of adolescents and adults across Malaysia. The 147-item FFQ was constructed using commonly consumed foods from five main ethnicities (Malay, Chinese, Indian, and Sabah and Sarawak indigenous groups) identified from national surveys. A cross-sectional validation study was conducted among purposively sampled healthy individuals aged 10–59 years from 16 administrative regions. Trained community nutritionists administered the FFQ to assess monthly intake, alongside a three-day dietary record and recall (3DRR) covering two weekdays and one weekend. Spearman’s correlation, Bland–Altman plots, and quartile cross-classification evaluated the agreement between the FFQ and 3DRR for energy, macronutrients, and selected micronutrients (Vitamin C, thiamine, calcium, and iron). Respondents (n = 361; 50.3% adults, 49.7% adolescents) were 50.4% female and represented five main ethnicities (range: 15.8–25.2%), with 60.4% from Peninsular Malaysia. Energy intake estimated by the FFQ (median: 2285 kcal) was significantly higher than by the 3DRR (median: 1785 kcal; Wilcoxon p < 0.001). Spearman’s correlation coefficients observed for energy (crude r = 0.31), and selected nutrients (energy-adjusted r range: 0.19–0.38), along with <10% of extreme quartile misclassification indicated acceptable ranking ability and agreement for most nutrients. Bland–Altman plots indicated no proportional bias for energy and macronutrients. In conclusion, the FFQ is a valid tool for assessing dietary intake within the multi-ethnic Malaysian population nationwide.