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Background In Timor-Leste there have been intermittent and ineffective soil-transmitted helminth (STH) deworming programs since 2004. In a resource-constrained setting, having information on the geographic distribution of STH can aid in prioritising high risk communities for intervention. This study aimed to quantify the environmental risk factors for STH infection and to produce a risk map of STH in Manufahi district, Timor-Leste. Methodology/Principal findings Georeferenced cross-sectional data and stool samples were obtained from 2,194 participants in 606 households in 24 villages in the Manufahi District as part of cross sectional surveys done in the context of the “WASH for Worms” randomised controlled trial. Infection status was determined for Ascaris lumbricoides and Necator americanus using real-time quantitative polymerase chain reaction. Baseline infection data were linked to environmental data obtained for each household. Univariable and multivariable multilevel mixed-effects logistic regression analysis with random effects at the village and household level were conducted, with all models adjusted for age and sex. For A. lumbricoides, being a school-aged child increased the odds of infection, whilst higher temperatures in the coolest quarter of the year, alkaline soils, clay loam/loam soils and woody savannas around households were associated with decreased infection odds. For N. americanus, greater precipitation in the driest month, higher average enhanced vegetation index, age and sandy loam soils increased infection odds, whereas being female and living at higher elevations decreased the odds of infection. Predictive risk maps generated for Manufahi based upon these final models highlight the high predicted risk of N. americanus infection across the district and the more focal nature of A. lumbricoides infection. The predicted risk of any STH infection is high across the entire district. Conclusions/Significance The widespread predicted risk of any STH infection in 6 to 18 year olds provides strong evidence to support strategies for control across the entire geographical area. As few studies include soil texture and pH in their analysis, this study adds to a growing body of evidence suggesting these factors influence STH infection distribution. This study also further supports that A. lumbricoides prefers acidic soils, highlighting a potential relatively unexplored avenue for control. Trial registration ClinicalTrials.gov ACTRN12614000680662., Author summary The majority of soil-transmitted helminth (STH) infections have long-term ramifications on an individual’s health and productivity, contributing to malnutrition, anaemia, and impaired childhood growth. In Timor-Leste there have been intermittent and ineffective STH control programs since 2004. When resources are constrained, having information on the geographic distribution of STH is important to ensure limited resources are targeted to areas most in need. In this study we predicted the risk of Ascaris lumbricoides, Necator americanus and any STH infection in the Manufahi district of Timor-Leste, providing the first available risk maps for STH infection in any part of the country. To achieve this, we assessed the relationship between selected environmental factors and STH infection to create multivariable models accounting for potential clustering of infections in villages and households. Using these multivariable models, we predicted the risk of A. lumbricoides and N. americanus infection across the district based on the environmental variables. We found that the predicted risk of infection with N. americanus in the age group older than 18 years of age and with any STH in 6–18 year olds was high and widespread across Manufahi, supporting the need for control strategies across the entire geographical region. Our study also highlighted the focal nature of A. lumbricoides infection and its relationship with soil pH.