User-friendly, evidence-based scientific tools to support sanitation decisions are still limited in the water, sanitation and hygiene (WASH) sector. This commentary provides lessons learned from the development of two sanitation decision support tools developed in collaboration with stakeholders in Uganda. We engaged with stakeholders in a variety of ways to effectively obtain their input in the development of the decision support tools. Key lessons learned included: tailoring tools to stakeholder decision-making needs; simplifying the tools as much as possible for ease of application and use; creating an enabling environment that allows active stakeholder participation; having a dedicated and responsive team to plan and execute stakeholder engagement activities; involving stakeholders early in the process; having funding sources that are flexible and long-term; and including resources for the acquisition of local data. This reflection provides benchmarks for future research and the development of tools that utilize scientific data and emphasizes the importance of engaging with stakeholders in the development process.