There are many issues in spatial planning in Indonesia. From 2010 to 2014, an Integrated Natural Resource Management project, “To establish more collaborative and equitable spatial plan leading to the design of new institutional arrangements, while ensuring more secure land tenure and community rights”, was conducted at the regency level in West Kalimantan and the Moluccas. The project aimed to develop an engagement strategy with stakeholders; improve communication linkages across decision levels, and collect detailed spatial, social, cultural and ecological data in line with large-scale mapping and the needs for new land allocation and policies in natural resource management. Results from the CoLUPSIA Participatory Prospective Analysis, livelihood and environment surveys are discussed. Land cover maps (large scale) and newly derived land allocation maps will impact the OneMap initiative of the Government and the local, provincial and national spatial plans that need revising. Lessons learned are discussed as well as the numerous remaining challenges in trying to promote a bottom-up approach in INRM.