Biomass combustion is an important source of black carbon (BC), yet the phase-resolved molecular patterns accompanying black-carbon evolution remain poorly constrained. In particular, detectable molecular signal abundance may not track black-carbon concentration across combustion conditions. Here, we investigated how detectable molecular profiles covary with BC by combining real-time measurements from a proton transfer reaction time-of-flight mass spectrometer (PTR-TOF-MS), for both gas-phase and particle-associated organics, with simultaneous aethalometer (AE-33) BC readings. Experiments were conducted across two biomass fuels (wheat straw and poplar wood) and three ignition temperatures (300, 500, and 700 °C). More than 200 retained nominal-m/z features were classified, and a prespecified block-level screen selected four BC-associated marker families, including furan-ring fragments, oxygenated aromatic, single-ring aromatic (SRA), and polycyclic aromatic hydrocarbons (PAHs), represented by 12 molecular markers. Particle-associated family signals show stronger within-event associations with BC (median block-level Spearman ρ = 0.86–0.92) than corresponding gas-phase signals. Particle-phase molecular profiles improve out-of-experiment BC prediction, increasing R² from 0.29 to 0.56 beyond a baseline model containing fuel, ignition temperature, and modified combustion efficiency. However, increasing ignition temperature enhanced BC production without a proportional increase in detectable BC-linked marker abundance, indicating a temperature-driven shift from precursor accumulation toward a more conversion-dominated regime. The molecular changes accompanying BC enhancement were fuel-specific, reflecting distinct marker compositions. These findings suggest that biomass BC formation is influenced not simply by detectable marker signal, but by temperature-dependent transformation of fuel-specific molecular pools, providing new constraints for interpreting molecular precursors in biomass-derived BC formation.