Background Despite the significant success of deworming programs in reducing morbidity due to soil-transmitted helminth (STH) infections globally, efforts to achieve elimination of STH as a public health problem or to potentially interrupt transmission will require improving and intensifying surveillance. However, non-participation in surveillance threatens the ability of programs to adequately monitor program status and limited research has been conducted to investigate drivers of non-participation in stool-based surveillance. Methodology/Principal findings This mixed-methods exploratory sequential study took place in Comé, Benin in association with the DeWorm3 Project. Six focus group discussions were conducted with individuals invited to participate in annual DeWorm3 stool surveillance. Thematic analysis was used to identify facilitators and barriers to participation and inform the quantitative analysis. A mixed-effects logistic regression model was built using baseline DeWorm3 survey data to identify factors associated with non-participation. Qualitative and quantitative findings were merged for interpretation. Among the 7,039 individuals invited to participate in baseline stool surveillance, the refusal rate was 8.1%. Qualitative themes included: community members weighing community-level benefits against individual-level risks, circulating rumors about misuse of stool samples, interpersonal communication with field agents, and cultural norms around handling adult feces. The quantitative analysis demonstrated that adults were significantly less likely to provide a stool sample than school-aged children (OR:0.69, 95%CI: 0.55–0.88), a finding that converged with the qualitative results. Individuals from areas in the highest quartile of population density were more likely to refuse to participate (OR:1.71, 95%CI:1.16–2.52). Several variables linked to community-affinity aligned with qualitative results; residing mainly in the community (OR:0.36, 95%CI:0.20–0.66) and having lived in the community for more than 10 years (OR:0.82, 95%CI:0.54–1.25) decreased likelihood of refusal. Conclusions/Significance Optimizing STH surveillance will require that programs reimagine STH surveillance activities to address community concerns and ensure that no subpopulations are inadvertently excluded from surveillance data.