Underutilized fruit (UF) species in Indonesia offer a wealth of nutritional value, unique secondary metabolites, and resilience to environmental changes, yet their use remains limited due to various barriers. This manuscript examines the diversity, potential applications, challenges, and conservation strategies for UF species across Indonesia. Representing a broad spectrum of botanical diversity, UF species embody Indonesia’s rich plant heritage and its ecological ties to global biodiversity. These fruits hold significant promise for enhancing food security, environmental sustainability, climate adaptation, cultural preservation, economic growth, and green urban planning. Despite these benefits, UF species face significant challenges, including socio-economic obstacles, environmental threats, and policy gaps that hinder their broader adoption and effective use. To address these issues, we propose a strategic framework that begins with a detailed inventory of UF species across Indonesian regions and their nutritional profiles. This framework advocates for increasing market demand by improving infrastructure, raising public awareness, and enhancing education. Further, collaborative research and community engagement are key to integrating UF species into sustainable practices. Together, these measures provide policymakers with a comprehensive basis for making informed decisions that support the conservation and utilization of Indonesia’s valuable UF species.