The food frequency questionnaire (FFQ) and the food record (FR) are among the most common methods used in dietary research. It is important to know that is it possible to use both methods simultaneously in dietary assessment and prepare a single, comprehensive interpretation. The aim of this study was to compare the energy and nutritional value of diets, determined by the FFQ and by the three-day food records of young women. The study involved 84 female students aged 21–26 years (mean of 22.2 ± 0.8 years). Completing the FFQ was preceded by obtaining unweighted food records covering three consecutive days. Energy and nutritional value of diets was assessed for both methods (FFQ-crude, FR-crude). Data obtained for FFQ-crude were adjusted with beta-coefficient equaling 0.5915 (FFQ-adjusted) and regression analysis (FFQ-regressive). The FFQ-adjusted was calculated as FR-crude/FFQ-crude ratio of mean daily energy intake. FFQ-regressive was calculated for energy and each nutrient separately using regression equation, including FFQ-crude and FR-crude as covariates. For FR-crude and FFQ-crude the energy value of diets was standardized to 2000 kcal (FR-standardized, FFQ-standardized). Methods of statistical comparison included a dependent samples t-test, a chi-square test, and the Bland-Altman method. The mean energy intake in FFQ-crude was significantly higher than FR-crude (2740.5 kcal vs. 1621.0 kcal, respectively). For FR-standardized and FFQ-standardized, significance differences were found in the mean intake of 18 out of 31 nutrients, for FR-crude and FFQ-adjusted in 13 out of 31 nutrients and FR-crude and FFQ-regressive in 11 out of 31 nutrients. The Bland-Altman method showed an overestimation of energy and nutrient intake by FFQ-crude in comparison to FR-crude, e.g., total protein was overestimated by 34.7 g/day (95% Confidence Interval, CI: −29.6, 99.0 g/day) and fat by 48.6 g/day (95% CI: −36.4, 133.6 g/day). After regressive transformation of FFQ, the absolute difference between FFQ-regressive and FR-crude equaled 0.0 g/day and 95% CI were much better (e.g., for total protein 95% CI: −32.7, 32.7 g/day, for fat 95% CI: −49.6, 49.6 g/day). In conclusion, differences in nutritional value of diets resulted from overestimating energy intake by the FFQ in comparison to the three-day unweighted food records. Adjustment of energy and nutrient intake applied for the FFQ using various methods, particularly regression equations, significantly improved the agreement between results obtained by both methods and dietary assessment. To obtain the most accurate results in future studies using this FFQ, energy and nutrient intake should be adjusted by the regression equations presented in this paper.