Anaerobic Digestion (AD) of wastewater for hydrogen production is a promising technology resulting in the generation of value-added products and the reduction of the organic load of wastewater. The Two-Stage Anaerobic Digestion (TSAD) has several advantages over the conventional single-stage process due to the ability to control the acidification phase in the first bioreactor, preventing the overloading and/or the inhibition of the methanogenic population in the second bioreactor. To carry out any process research and process optimization, adequate mathematical models are required. To the best of our knowledge, no mathematical models of TSAD have been published in the literature so far. Therefore, the authors’ motivation is to present a high-quality model of the TSAD corn steeping process for the sequential production of H2 and CH4 considered in this paper. Four metaheuristics, namely Genetic Algorithm (GA), Firefly Algorithm (FA), Cuckoo Search Algorithm (CS), and Coyote Optimization Algorithm (COA), have been adapted and implemented for the first time for parameter identification of a new nonlinear mathematical model of TSAD of corn steep liquor proposed here. The superiority of some of the algorithms has been confirmed by a comparison of the observed numerical results, graphical results, and statistical analysis. The simulation results show that the four metaheuristics have achieved similar results in modelling the process dynamics in the first bioreactor. In the case of modelling the second bioreactor, a better description of the process dynamics trend has been obtained by FA, although GA has acquired the lowest value of the objective function.