Native fruits, often adapted to local environments and rich in bioactive compounds, offer untapped potential to enhance food security, dietary diversity, and sustainable development, particularly in biodiversity-rich regions. However, scientific research on these species remains limited and fragmented. This study aimed to map global research trends on native fruits through a bibliometric and text mining analysis of 989 articles indexed in Scopus from 2001 to 2023. Results reveal a steady growth in scientific production, especially in the last decade, driven by the Sustainable Development Goals (SDGs), public health concerns, and the socioeconomic and environmental significance of native species. Brazil stands out as the leading contributor, with notable participation from countries such as Australia, Spain, the United States, and China, supported by international collaboration networks. Research hotspots include genetic studies, cultural valuation, chemical and sensory profiling, phytochemical composition, particularly phenolics and antioxidants, and other functional properties. Despite this progress, several barriers persist: limited species prioritization, knowledge gaps, insufficient processing technologies, lack of compositional data, and underutilization of by-products. The findings offer valuable insights for researchers, policymakers, entrepreneurs, and communities seeking to conserve, utilize, and promote native fruits within sustainable food systems.