Reflecting on our journey in developing the decision support system (DSS) and our prior limited experience in its construction, we have identified several key lessons that can benefit future researchers aiming to develop DSS. The reflections are categorized into six areas: project timeframe and funding; thorough and adaptive planning; power of data and uncertainties; legitimacy and equity; participatory vs data-driven decision-making; and policy implications. At the end of the chapter, we illustrate further potential applications of the developed DSS in supporting the decision-making process in the study area. In the pre- and during the project timeframes, we emphasize the importance of professional and holistic research fund management, adaptive planning using an open framework approach, and the selection of professional and capable team members, which may be appropriate for all projects funded by the Global South Government. At the theoretical level, we reflected on the challenges to integrate participatory and evidence-based management and listed several important suggestions to improve their integration. We also contemplated the challenges and solutions to balance legitimacy and credibility in the DSS. We expect that our lessons learned will aid in improving future ecosystem decision-making-related projects.