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Background: Childhood obesity is a multifactorial disease. Most of these factors start to develop before birth and worsen throughout life. Therefore, prevention efforts should begin in the first 1000 days of life. This study aimed to quantify published studies on risk factors according to the Six-Cs model of childhood obesity (cell, child, clan, culture, community, and country) and determine which of them have been related to anthropometric indicators of overweight or obesity in children under 2 years of age in Mexico. Methods: A systematic scoping review (PRISMA-ScR) was performed. PubMed, Scopus, and EBSCOhost databases were reviewed. Results: We found that 88% of the studies were observational. The child and family spheres were the most studied, individually and as a whole. The least studied were community, culture, and country. The main risk factors related to obesity indicators were high birth weight, birth by cesarean section, and inadequate feeding practices, in addition to mothers with obesity and those who underestimate their child’s weight, stressful parenting style, and food insecurity in the home, together with living in urban areas, family income, and beliefs about preference for ultra-processed products. Conclusion: In Mexico, the study of obesity in early childhood is emerging at the research level. However, further efforts are required to close the knowledge gap at the socioecological level to design evidence-based interventions and reduce early obesity.