Most epidemiological studies of soil-transmitted helminth (STH) infections focus on school-going children. The majority of large-scale cross-sectional and longitudinal community-based studies have been conducted prior to the implementation of wide-scale mass drug administration (MDA). This study investigates age-related patterns in prevalence and intensity of STH infection, and associated risk factors, in a region of south coastal Kenya that had previously received three consecutive years of school-based deworming (2012–14) and four rounds of community-based MDA for lymphatic filariasis between 2003 and 2014. Between March and May 2015, a cross-sectional survey was conducted in 120 community clusters as a baseline for a cluster randomised trial. Individuals aged two years and above were randomly selected during household surveys and requested to provide stool samples, which were assessed for presence and intensity of STH using the duplicate Kato-Katz thick smear method. Species-specific predictors of presence and intensity were investigated through multilevel logistic regression and zero-inflated negative binomial regression models. Of the 19,684 individuals who provided a stool sample, 21.5% were infected with at least one STH. Hookworm was the predominant species, with an overall prevalence of 19.1%; Trichuris trichiura prevalence was 3.6% and Ascaris lumbricoides was negligible (0.4% prevalence). The vast majority were light intensity infections. Prevalence and intensity of hookworm infection were significantly higher in adults and males, and were associated with environmental conditions, low socio-economic status, household flooring, individual and household water, sanitation and hygiene (WASH) characteristics and behaviours, previous treatment, lack of shoe-wearing and not attending school. In contrast, T. trichiura was more commonly found in school-aged boys and those living in communities close to the coast, with reduced infection in the least poor individuals with private latrine access. Overall, results show that despite several years of school-based deworming, hookworm infection remains common among untreated adults in this population, suggesting that this strategy alone is insufficient to reduce community-wide hookworm infection and in the longer term to eliminate transmission.