Background/Objectives: Dietary habits have a major role in obesity, type 2 diabetes and atherosclerotic cardiovascular diseases. In this study, we compared the effects of sea buckthorn (SB) and its fractions, and bilberries (BBs) on associated variables of metabolic diseases on overweight and obese women. Subjects/Methods: In total, 110 female volunteers were recruited, and they followed four different berry diets (BB, SB, SB phenolic extract (SBe) and SB oil (SBo)) in a randomized order for 33-35 days. Each intervention was followed by a wash-out period of 30-39 days. Blood samples were drawn and physical measurements were performed after each period. Eighty volunteers completed the study. Results: There was statistically significant decrease in waist circumference after BB (D, À1.2 cm; P ¼ 0.041) and SB (D, À1.1 cm; P ¼ 0.008) periods and also a small decrease in weight after BB diet (D, À0.2 kg; P ¼ 0.028). Vascular cell adhesion molecule decreased after BB (D, À49.8 ng/ml; P ¼ 0.002) and SBo (D, À66.1 ng/ml; P ¼ 0.001) periods, and in intercellular adhesion molecule (ICAM) after SBe diet (D, À6.1 ng/ml; P ¼ 0.028). Conclusions: Based on the results, it can be stated that different berries and berry fractions have various but slightly positive effects on the associated variables of metabolic diseases.