Obesity is considered one of the biggest health problems of the 21st century, becoming a worldwide epidemic, leading to the development of many diseases and increasing the risk of premature death. The first step in reducing body weight is a calorie-restricted diet. To date, there are many different diet types available, including the ketogenic diet (KD) which is recently gaining a lot of attention. However, all the physiological consequences of KD in the human body are not fully understood. Therefore, this study aims to evaluate the effectiveness of an eight-week, isocaloric, energy-restricted, KD as a weight management solution in women with overweight and obesity compared to a standard, balanced diet with the same calorie content. The primary outcome is to evaluate the effects of a KD on body weight and composition. The secondary outcomes are to evaluate the effect of KD-related weight loss on inflammation, oxidative stress, nutritional status, profiles of metabolites in breath, which informs about the metabolic changes in the body, obesity and diabetes-associated parameters, including a lipid profile, status of adipokines and hormones. Notably, in this trial, the long-term effects and efficiency of the KD will be studied. In summary, the proposed study will fill the gap in knowledge about the effects of KD on inflammation, obesity-associated parameters, nutritional deficiencies, oxidative stress and metabolism in a single study.ClinicalTrail.gov registration number:NCT05652972.