The food frequency questionnaire (FFQ) is designed to capture an individual’s habitual dietary intake and is the most applied method in nutritional epidemiology. Our aim was to assess the relative validity and reproducibility of the FFQ used in the Diet, Cancer, and Health—Next Generations cohort (DCH-NG). We included 415 Danish women and men aged 18–67 years. Spearman’s correlations coefficients, Bland–Altman limits of agreement and cross-classification between dietary intakes estimated from the FFQ administered at baseline (FFQ_baseline), and the mean of three 24-h dietary recalls (24-HDRs) and the FFQ administered after 12 months (FFQ_{12 months}) were determined. Nutrient intakes were energy-adjusted by Nutrient Density and Residual methods. Correlation coefficients ranged from 0.18–0.58 for energy and energy-adjusted nutrient intakes, and the percentage of participants classified into the same quartile ranged from 28–47% between the FFQ_baseline and the 24-HDRs. For the FFQ_{12 months} compared with FFQ_baseline, correlation coefficients ranged from 0.52–0.88 for intakes of energy, energy-adjusted nutrients, and food groups, and the proportion of participants classified into the same quartiles ranged from 43–69%. Overall, the FFQ provided a satisfactory ranking of individuals according to energy, nutrient, and food group intakes, making the FFQ suitable for use in epidemiological studies investigating diet in relation to disease outcomes.