Hydrogen is becoming recognized as a clean and sustainable energy carrier, with microbial fermentation and electrolysis serving critical roles in its production. This paper provides a thorough meta-analysis of BioH2 production across diverse substrates, microbial populations, and experimental settings. Statistical techniques, including ANOVA, principal component analysis (PCA), and heatmaps, were used to evaluate the influence of various parameters on the hydrogen yield. The mean hydrogen generation from the reviewed studies was 168.57 ± 52.09 mL H2/g substrate, with food waste and glucose demonstrating considerably greater hydrogen production than mixed food waste (p < 0.05). The inhibition of methanogens with inhibitors like 2-bromoethanesulfonate (BES) and chloramphenicol (CES) enhanced hydrogen production by as much as 25%, as demonstrated in microbial electrolysis cell systems. PCA results highlighted Clostridium spp., Thermotoga spp., and Desulfovibrio spp. as the most dominant microbial species, with Clostridium spp. contributing up to 80% of the YH2 in fermentation systems. The study highlights synergistic interactions between dominant and less dominant microbial species under optimized environmental conditions (pH 5.5–6.0, 65 °C), emphasizing their complementary roles in enhancing H2 production. Volatile fatty acid regulation, particularly acetate and butyrate accumulation, correlated positively with hydrogen production (r = 0.75, p < 0.01). These findings provide insights into optimizing biohydrogen systems through microbial consortia management and substrate selection, offering a potential way for scalable and efficient H2 production.