This study presents a detailed analysis of the thermal degradation and kinetic behavior of two Amazonian wood species, Goupia glabra (cupiúba) and Manilkara huberi (maçaranduba), using thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), Fourier-transform infrared spectroscopy (FTIR-ATR), and direct infusion mass spectrometry (DIMS). Wood samples were subjected to controlled heating rates of 20, 40, and 60 °C/min from 25 to 800 °C under an argon atmosphere. TGA revealed moisture evaporation below 120 °C, with hemicellulose degradation occurring between 220 and 315 °C, cellulose decomposition between 315 and 400 °C, and lignin breakdown over a broader range from 180 to 900 °C. The highest rate of mass loss occurred at 363.99 °C for G. glabra and 360.27 °C for M. huberi at a heating rate of 20 °C/min, with shifts to higher temperatures at faster heating rates. Activation energies were calculated using Arrhenius and Kissinger models, yielding values between 53.46–61.45 kJ/mol for G. glabra and 58.18–62.77 kJ/mol for M. huberi, confirming their stable thermal profiles. DSC analysis identified a significant endothermic peak related to moisture evaporation below 100 °C, followed by two exothermic peaks. For G. glabra, the first exothermic peak appeared at 331.45 °C and the second at 466.08 °C, while for M. huberi, these occurred at 366.41 °C and 466.08 °C, indicating the decomposition of hemicellulose, cellulose, and lignin. Enthalpy values for G. glabra were 12,633.37 mJ and 18,652.66 mJ for the first and second peaks, respectively, while M. huberi showed lower enthalpies of 9648.04 mJ and 14,417.68 mJ, suggesting a higher energy release in G. glabra. FTIR-ATR analysis highlighted the presence of key functional groups in both species, with strong absorption bands in the 3330–3500 cm−1 region corresponding to O-H stretching vibrations, indicative of hydroxyl groups in cellulose and hemicellulose. The 1500–1600 cm−1 region, representing aromatic C=C vibrations, confirmed the presence of lignin. Quantitatively, these results suggest a high content of cellulose and lignin in both species. DIMS analysis further identified polyphenolic compounds and triterpenoids in M. huberi, with major ions at m/z 289 and 409, while G. glabra showed steroidal and polyphenolic compounds with a base peak at m/z 395. These findings indicate the significant presence of bioactive compounds, contributing to the wood’s resistance to microbial degradation. This comprehensive thermal and chemical characterization suggests that both species have potential industrial applications in environments requiring high thermal stability.