The paper reports the results of a long term (310 days) pilot-scale trial where food waste as sole substrate was treated in a two-phase thermophilic anaerobic digestion process. This was optimized for concurrent hydrogen and methane production. First phase's optimization for hydrogen production was obtained recirculating the effluent coming from the methanogenic phase and without the addition of external chemicals. A drawback of such approach is the recirculation of ammonia into the first phase reactor for hydrogen production with possibility of consequent inhibition. Therefore this study was focused on the development of a control protocol based on ammonia concentration. The first part of this paper illustrates how the use of a variable recirculation flow makes possible to control the whole process, preventing the ammonia inhibition in the system. In order to lay down the groundwork for an automatic control of the process, in the second part of the study a preliminary statistical study is presented. In the latter are developed models to predict ammonia levels in system using the measure of Electrical Conductivity, Volatile Fatty Acids and Alkalinity. During steady state conditions, managed by a variable recirculation flow, the system produced a mixture of gas that met the standards for the biohythane mix with an average composition range of 7% H-2, 58% CH4 and 35% CO2. The overall average specific gas production (SGP) reached 0.69 M-Biogas(3)/kgTVS and gas production rate (GPR) of 2.78 m(3)/m(r)(3)d. Copyright (C) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.