Abstract Objectives Chronic malnutrition and anemia are prevalent in developing countries. This research aimed to determine the prevalence of chronic malnutrition and anemia and their associated factors in children under five using a multi-causal model in a rural community in the coast of Ecuador. Methods The study included 314 children under 5 years old who were residents of San Isidro, Ecuador. Indicators of chronic malnutrition and anemia were identified. Mothers/caregivers were surveyed on socio-economic and environmental conditions, feeding and care practices, access to health services and biological characteristics. Bivariate and multivariable Poisson regression were performed. Results The prevalence was 12.42% (n = 39) for chronic malnutrition and 16.98% (n = 54) for anemia. There was a significant and independent association between chronic malnutrition and family income less than $80 USD per month (Prevalence Ratio [PR] = 2.74, 95% CI 1.04, 7.20), maternal height less than 150 cm (PR 3.00, 95% CI 1.69, 5.32) and residence in a household with more than 4 children (PR 3.05, 95% CI 1.48, 6.29). Anemia was 2.57 times higher (95% CI 1.17, 5.65) in children with more than two episodes of diarrhea in the last 6 months. Prenatal care (5 to 8 visits) provided a protective effect for anemia (PR 0.48, 95% CI 0.27, 0.89). Conclusions for Practice Findings support the need for comprehensive interventions targeted toward chronic malnutrition and anemia in children from rural coastal communities. Improvement of socioeconomic conditions, family planning, prenatal care and reduction of diarrheal diseases should be prioritized.