This study investigates the potential of using Jerusalem artichoke (JA) and bakery waste (BW) for biogas and biohydrogen production through dark fermentation. The experiment included four series with different ratios of JA to BW (100:0, 0:100, 50:50, 75:25) under mesophilic conditions at 39 °C. The highest biogas (1.46 L/L.d) and hydrogen production (0.508 L/L.d) was achieved with BW alone. A synergistic effect was observed with the 50:50 mixture, resulting in the highest production of volatile fatty acids (VFA), which reached up to 22252 mg/L. This shows the advantages of combining these substrates for optimized energy production. Spearman rank correlation analysis identified ammonium-nitrogen (N-NH4) as the most influential factor and showed a strong positive correlation with butyric acid/acetic acid (B/A) ratio (ρ = 0.85, p < 0.001). This indicates that maintaining optimal ammonium-nitrogen levels is critical for maximizing yields. In addition, total solids (TS) and volatile solids (VS) showed moderate positive correlations with specific VFAs, indicating their significant role in VFA dynamics. These results highlight the importance of substrate optimization and maintaining stable fermentation conditions for sustainable and efficient energy production.