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The structure and properties of polymer-derived Si–(B–)OC glasses have been shown to be significantly influenced by the boron content and pyrolysis temperature. This work determined the impact of these two parameters on the thermodynamic stability of these glasses. High-temperature oxide melt solution calorimetry was performed on a series of amorphous samples, with varying boron contents (0–7.7 at.%), obtained by pyrolysis of precursors made by a sol–gel technique. Thermodynamic analysis of the calorimetric results demonstrated that at a constant pyrolysis temperature, adding boron makes the materials energetically less stable. While the B-containing glasses pyrolyzed at 1000°C were energetically less stable than the competitive crystalline components, increasing the pyrolysis temperature to 1200°C led to their enthalpic stability. 29Si and 11B MAS nuclear magnetic resonance (NMR) spectroscopy measurements on selected samples confirmed a decrease in the concentrations of mixed Si-centered SOiC4−i and B-centered BOjC3−j bonds at the expense of formation of SiO4 and B(OSi)3 species (indicating a tendency toward phase separation) when the boron content and pyrolysis temperature increased. In light of the findings from calorimetry and NMR spectroscopy, we propose a structure–energetic relationship in Si–(B–)OC glasses.