Weight loss diets affect food choices and control of eating. We evaluated the effects of intermittent energy restriction (IER) vs. continuous energy restriction (CER) on nutritional composition and eating behavior. Individuals with BMI 30-45 kg/m2, abdominal obesity and ≥1 additional metabolic syndrome component were randomized to IER vs. CER with similar energy restriction. Of 112 participants, 98 completed weighed dietary records and the Three Factor Eating Questionnaire at baseline and three months. In statistical analysis, changes were adjusted for baseline values. Weight loss, energy intake, and macronutrient composition were similar in the IER and CER groups. The CER group reported a greater increase in fruit and berries (45 g/day [95% CI 21, 71] vs. 2 g/day [-28, 33]; p = 0.047) and vegetables (135 g/day [91, 179] vs. 65 g/day [35, 96]; p = 0.010) than the IER group. Fiber intake increased in the CER compared to the IER group (1.0 g/MJ/day [0.8, 1.2] vs. 0.2 [0.0, 0.4]; p < 0.001). Sugar intake was reduced in the CER compared to the IER group (-2.2E% [-3.2, -2.2] vs. -0.1E% [-1.2, 1.0]; p = 0.007). Intakes of folate, potassium, and magnesium decreased more in the IER than the CER group, while vitamin C increased more in the CER group (all p-values <0.014). Both diets improved eating behavior scores, but cognitive restraint increased more in the CER than the IER group (34 [30, 39] vs. 17 [12, 22]; p = 0.013). Men and women with obesity had more favorable changes in nutritional composition and eating behavior with CER than IER.