Anaerobic co-digestion in wastewater treatment plants is looking increasingly like a straightforward solution to many issues arising from the operation of mono-digestion. Process modelling is relevant to predict plant behavior and its sensitivity to operational parameters, and to assess the feasibility of simultaneously feeding a digester with different organic wastes. Still, much work has to be completed to turn anaerobic digestion modelling into a reliable and practical tool. Indeed, the complex biochemical processes described in the ADM1 model require the identification of several parameters and many analytical determinations for substrate characterization. A combined protocol including batch Biochemical Methane Potential tests and analytical determinations is proposed and applied for substrate influent characterization to simulate a pilot-scale anaerobic digester where co-digestion of waste sludge and expired yogurt was operated. An iterative procedure was also developed to improve the fit of batch tests for kinetic parameter identification. The results are encouraging: the iterative procedure significantly reduced the Theil’s Inequality Coefficient (TIC), used to evaluate the goodness of fit of the model for alkalinity, total volatile fatty acids, pH, COD, volatile solids, and ammoniacal nitrogen. Improvements in the TIC values, compared to the first iteration, ranged between 30 and 58%.