Background: Childhood obesity is one of the greatest public health problems facing advanced societies, and Spain is one of the countries with the highest incidence. There are many studies that monitor at the national level, but given the lack of specificity, lack of updating and scarcity of epidemiological data on overweight, obesity, physical condition and well-being of children and adolescents in Extremadura, it seems necessary to create a Well-being, Obesity and Motricity Observatory in Childhood and Youth (WOMO) in Extremadura in order to follow up on the evolution of this problem and to propose strategies to combat it. Therefore, this project aims (1) to obtain information on the physical condition, body composition and well-being of children and youth in Extremadura every year and (2) to evaluate the relationship between obesity, overweight, physical condition, well-being, self-perceived physical fitness, physical activity adherence, physical literacy, health-related quality of life (HRQoL), happiness and satisfaction with life, connection with nature, barriers to sports practice, self-concept and bullying in children and youth. Methods: An annual monitoring cross-sectional and follow-up study will be performed. Primary outcome measures will be (1) personal data and anthropometric measurements, (2) family and school information, (3) physical condition, (4) obesity and overweight level, and (5) well-being. Secondary outcome measures will be (1) self-perceived physical fitness, (2) physical activity adherence, (3) physical literacy, (4) HRQoL, (5) happiness and satisfaction with life, (6) connection with nature, (7) barriers to sports practice, (8) self-concept and (9) bullying. Discussion: This project will provide valuable information to adopt appropriate strategies to reduce the level of overweight and obesity in children and youth. Furthermore, orientations will be given to transfer the results obtained to the business sector or to the public sector to evaluate or change the policies adopted.