Dark fermentation is a promising biological method for hydrogen production, utilizing anaerobic bacteria to break down organic substrates. Despite its potential, several techno-economic barriers hinder its large-scale commercialization. These challenges span technical, economic, and infrastructural domains, limiting its competitiveness compared to conventional hydrogen production methods.

One of the most significant technical barriers is the low hydrogen yield. Dark fermentation typically achieves yields of 1–2 mol H₂/mol glucose, far below the theoretical maximum of 4 mol H₂/mol glucose. This inefficiency stems from metabolic limitations, where bacteria divert carbon toward byproducts like acetic acid, butyric acid, and ethanol instead of hydrogen. The presence of hydrogen-consuming microbes further reduces net output. While metabolic engineering and optimized reactor designs aim to improve yields, achieving consistent, high-performance systems remains elusive.

Pretreatment of feedstocks presents another major hurdle. Many organic substrates, such as lignocellulosic biomass, require extensive physical, chemical, or enzymatic pretreatment to enhance biodegradability. These processes are energy-intensive and costly, often accounting for a substantial portion of operational expenses. For example, acid or alkali pretreatment generates waste streams that require neutralization, adding to disposal costs. Enzymatic methods, though milder, involve expensive biocatalysts. Reducing pretreatment costs without compromising efficiency is critical for improving economic viability.

The variability of feedstocks also complicates process stability. Dark fermentation can utilize diverse organic wastes, including agricultural residues, food waste, and industrial effluents. However, the composition of these materials fluctuates, leading to inconsistent hydrogen production. Contaminants like heavy metals or inhibitory compounds may further disrupt microbial activity. Standardizing feedstock quality or developing robust microbial consortia capable of handling diverse inputs is necessary to ensure reliable operation.

System scaling poses additional challenges. Laboratory-scale dark fermentation systems demonstrate feasibility, but translating these to industrial levels introduces complexities. Larger reactors face mass transfer limitations, uneven substrate distribution, and difficulties in maintaining optimal anaerobic conditions. Gas-liquid separation and purification further strain system design, as hydrogen must be efficiently extracted from mixed gas streams containing CO₂ and other volatiles. Without scalable reactor architectures, commercial deployment remains impractical.

Economic barriers are equally prohibitive. The capital expenditure for dark fermentation facilities is high, driven by the need for specialized reactors, gas handling systems, and pretreatment units. Operational costs, including energy for mixing, heating, and downstream processing, further erode profitability. Compared to steam methane reforming, which benefits from established infrastructure and economies of scale, dark fermentation struggles to compete on cost. Current estimates suggest hydrogen production via dark fermentation is 2–3 times more expensive than SMR, though regional feedstock availability may alter this balance.

Infrastructure gaps also impede commercialization. Unlike conventional hydrogen, which leverages existing natural gas pipelines and storage systems, dark fermentation lacks dedicated distribution networks. Hydrogen produced from decentralized fermentation plants requires compression or conversion into carriers like ammonia for transport, adding logistical expenses. The absence of refueling or industrial offtake agreements further restricts market access. Developing infrastructure tailored to biohydrogen is essential for fostering adoption.

Regulatory and certification challenges add another layer of complexity. Dark fermentation-derived hydrogen must meet purity standards for industrial or fuel cell applications, necessitating additional purification steps. However, standardized protocols for biohydrogen quality are still evolving. Uncertainties around lifecycle emissions accounting and sustainability certification also deter investors. Clear policies defining green hydrogen thresholds and incentivizing bio-based production could mitigate these risks.

Research and development gaps persist in critical areas. While advances in microbial strain selection and genetic engineering show promise, translating lab breakthroughs to commercial systems is slow. Integration with downstream processes, such as coupling dark fermentation with photofermentation or anaerobic digestion to boost yields, requires further optimization. Additionally, real-world data on long-term system performance under varying conditions is scarce, hindering investor confidence.

Despite these barriers, dark fermentation holds unique advantages, such as utilizing low-value waste streams and operating at ambient temperatures. Addressing the techno-economic challenges will require coordinated efforts in microbial science, reactor engineering, and policy support. Incremental improvements in yield, pretreatment efficiency, and system integration could gradually enhance competitiveness. However, without significant advancements in these areas, dark fermentation is likely to remain a niche player in the hydrogen economy.

The path forward involves targeted innovation to lower costs and improve reliability. Public-private partnerships could accelerate pilot demonstrations, while subsidies for feedstock preprocessing or carbon pricing on fossil-based hydrogen may improve economic feasibility. As the hydrogen market expands, dark fermentation may find specialized roles in waste-rich regions or circular economy frameworks, provided its core limitations are systematically addressed.

In summary, the commercialization of dark fermentation faces multifaceted obstacles, from biological inefficiencies to infrastructural deficits. Overcoming these will demand sustained investment in research, scalable technologies, and supportive policy frameworks to unlock its potential as a sustainable hydrogen source.