The global “nutrition transition” has increased children’s consumption of sugary snacks and beverages (junk food), compounding their risk for poor oral health and malnutrition. The purpose of this study was to examine the relationship between early childhood caries (ECC) and malnutrition in a community context. This is a baseline and two-year follow-up analysis of a community-based preventive oral health and nutrition intervention for 1,575 children, from birth through age six, in an indigenous population in rural Ecuador. Trained community volunteers, preschool teachers and dentists provided children and families with nutrition and oral health education, toothbrushes and fluoride toothpaste, fluoride varnish, and referral for dental treatment, three times per year. Annual data collection included mother interviews, child dental examinations and measurements of height and weight. Descriptive and bivariate analyses were completed in SPSS. At baseline, nearly half of children consumed junk food daily. ECC began in infancy, increasing steadily thereafter. Among one-year-olds, 53.8% had caries with a mean of 2.1 decayed teeth; and among six-year-olds, 98.6% had caries with a mean of 10.5 decayed teeth, and half experienced mouth pain. At two-year follow-up, reported junk food consumption was cut in half; and the prevalence and severity of caries and mouth pain were reduced. Children who entered the intervention in their first year of life experienced the greatest dental improvements. Children who entered in their first two years and attended the entire two-year intervention experienced a one-third reduction in stunting malnutrition, with greatest improvement among those whose caries increment was controlled. ECC and caries-related malnutrition were reduced for children who participated in this prevention-oriented community oral health and nutrition intervention, especially those beginning in the first two years of life. Oral health and nutrition promotion should be incorporated into all maternal-child health programs, from pregnancy and birth onward.