The purpose of this paper is to investigate, both theoretically and experimentally, hydrogen production from agro-industrial by-products using a continuous bioreactor packed with a mixture of spongy and glass beads and inoculated with Enterobacter aerogenes. Replicated series of experimental runs were performed to study the effects of residence time on hydrogen evolution rate and to characterize the critical conditions for the wash out, as a function of the inlet glucose concentration and of the fluid superficial velocity. A further series of experimental runs was focused on the effects of both residence time and inlet glucose concentration over hydrogen productivity. A kinetic model of the process was developed and showed good agreement with experimental data, thus representing a potential tool to design a large-scale fermenter. In fact, the model was applied to the optimal design of a bioreactor suitable of feeding a phosphoric acid fuel cell of a target power.