Thermophilic bacteria able to survive extreme temperature stress are of great biotechnological interest due to their extracellular production of bioactive molecules as a part of a survival strategy, or by intracellular modifications. In the present study, thermophilic Bacillus haynesii CamB6, isolated from a Chilean hot spring, was studied for the formation of different stress response molecules. The polymeric pigment produced by the bacterial strain was characterized by different physicochemical techniques. On exposure to ranges of temperature (50–60 °C), pH (5.0–7.0), and sources of nitrogen and carbon (1–5 g·L−1), the bacteria responded with a biofilm network formation in a hydrophobic polystyrene surface. Biofilm formation under fed-batch conditions was also statistically validated. The bacteria showed a planktonic pellicle network formation in the presence of induced hypoxia and salinity stress (19.45 g·L−1) under static conditions. Salinity stress also resulted in the intracellular response of brown pigment production. The pigment was structurally and functionally characterized by UV-Vis absorbance and the presence of different characteristic peaks via FTIR analysis (bacterial pyomelanin fingerprints) were assessed. A high thermal stability and TGA profile indicated the brown pigment was a probable pyomelanin candidate. Micropyrolysis (Py-GC/MS) showed that isoprene, pyrrole, benzene, pyridine, and their derivatives were the major components detected. In addition, acetic acid, indole, phenol, and its derivatives were observed. The absence of sulfocompounds in the pyrolyzed products agreed with those reported in the literature for pyomelanin. The pigment surface morphology was analyzed via SEM, and the elemental composition via EDS also demonstrated the similarity of the brown pigment to that of the melanin family. The pyomelanin pigment was observed to be bioactive with promising antioxidant capacity (H2O2, Fe2+) compared to the standard antioxidant molecules. In conclusion, B. haynesii CamB6 demonstrated the formation of several biomolecules as a stress response mechanism that is bioactive, showing its probable biotechnological applications in future.