Free, prior, and informed consent (FPIC) is a fundamental ethical principle in community-based research. It ensures participants are fully informed about a study’s purpose, risks, and benefits, and their involvement is voluntary and free from coercion. In participatory, community-based research, FPIC must be an ongoing process, reflecting an evolving research process and outcome. In rural Indonesia–and similar settings–effective FPIC processes for community-based research must align with local and Indigenous communities’ collective decision-making, which are often grounded in deliberative dialogue, local protocols, oral agreements, and trust-based, reciprocal relations. It is equally crucial to meaningfully engage marginalised groups who may not feel fully represented by community leaders, to ensure inclusive FPIC processes and decisions. This practice note details an intersectionally aware process for securing FPIC in a participatory project in Indonesia. It shares lessons learned and insights aimed at enhancing inclusive, community-based research and development initiatives around the world. © 2025 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.