The production of renewable energy, a reduction of waste and prevention of environmental pollution promote the industrial application of anaerobic co-digestion for the treatment of agro-industrial organic waste. In this paper production of biogas/methane was studied by performing a series of laboratory batch experiments using whey and cow manure as substrates. The influence of substrate concentration, temperature and pH on biogas production was analysed. A mathematical model has been developed that describes the co-digestion process. The hydrolysis of proteins, lipids and cellulose has been modelled using first-order kinetics. Fermentation of sugars and amino acids, anaerobic oxidation of long chain fatty acids (LCFA), acetogenesis and methanogenesis have been described using an unstructured model based on Monod kinetic equations taking into account different inhibitory effects. Model applicability was demonstrated by comparing experimental results with the model simulation results.