Background There is evidence of the occurrence of trachoma in Peru, and studies have shown that soil-transmitted helminthiases (STH) are affecting rural communities in the Amazon basin in Loreto Department. This study was done to estimate trachoma prevalence, STH preva-lence, and the associated factors for both diseases in children aged 1–9 years in rural communities of Peru. Methodology A population-based cross-sectional survey was carried out in rural communities of Loreto. A standardized survey questionnaire with individual and household risk factors related to both diseases was used. Ocular examination was done for all participants aged one year and above, and eye swab samples were collected from children with follicular trachoma (TF). Anthropometric measurements, stool samples for STH, and blood samples for hemoglobin measurement were taken from children. Principal findings TF prevalence was 7.74% (95% CI 5.08–11.63%), STH prevalence was 49.49% (95% CI 25.00–52.43%), and prevalence of co-occurrence of both diseases was 5.06% (95% CI 2.80–8.98%) in children aged 1–9 years. Being at age 3–8 years old (AOR = 6.76; 95% CI 1.346–33.947), have an unclean face (AOR = 24.64; 95% CI 6.787–89.444), and having been dewormed in the last six months (AOR = 2.47; 95% CI 1.106–5.514), were risk factors of TF. Being a female (AOR = 0.22; 95% CI 0.103–0.457) was associated with decreased odds of TF. Having been dewormed in the last six months (AOR = 0.30; 95% CI 0.139– 0.628) was a preventative factor for STH. Risk factors for children with both diseases mir-rored the findings for risk factors for individual diseases. Conclusions Neglected tropical diseases and associated risk factors overlap in communities living in vulnerable conditions in the Amazon basin of Peru. These findings support the need to imple-ment integrated interventions, including mass drug administration, water, sanitation, and hygiene for both diseases in the study area.