Increasing greenhouse gas emissions and its implications on climate change demand development of biofuels, whereof dark fermentative biohydrogen production and biogas production are promising routes. Regarding a future integration of those biofuel production systems under CO2-neutrality, a better understanding and quantification of the involved bioprocesses are required. The goal of this PhD-Thesis is the optimization and productivity increase of two biological systems for biofuels production, in particular biohydrogen and biogas. Therefore, the impacts of different working conditions, named process parameters and medium composition, on the physiological key parameters of these two fermentative anaerobic biosystems for biofuels production are evaluated. With this aim, it is important to establish a methodology to optimize the components and their concentrations in the required media. Furthermore, an increase of biomass productivity in those bioprocesses would allow for an increased production of the compound of interest, the corresponding biofuel. Within this context, an external cell retention system is studied and implemented for each of the bioprocesses discussed in this thesis.