This study evaluated the potential of Total Reflection X-ray Fluorescence (TXRF) as a geochemical traceability method for wood from Manilkara huberi (Ducke) A. Chev., a species of high commercial and ecological value widely exploited in the Legal Amazon. Wood samples were collected in eight locations in the states of Amazonas, Pará, Rondônia, and Roraima, representing different edaphic, geological, and climatic conditions in the context of Amazonian edaphic and geological variability. The multielemental analysis revealed significant variations in trace element and macronutrient concentrations (Fe, Mn, K, Ca, Sr, Rb), reflecting the specific geochemical signatures of each region. Multivariate analyses (PCA and NMDS) showed distinct groupings among the populations, confirming the discriminatory capacity of TXRF in the differentiation of geographical origins. Significant correlations between elements such as K × Rb and Cr × Fe demonstrated consistent patterns of coaccumulation and antagonism associated with local geochemistry. The results prove the efficiency of TXRF as a non-destructive, sensitive, and low-cost technique for origin authentication and forensic investigation of Amazonian wood, strengthening sustainable management policies and combating illegal exploitation. The proposed methodology is a scientific advance in forest traceability and biodiversity conservation, contributing to the transparency and legality of timber production chains in the Amazon.