Anaerobic mixed-culture fermentations are interesting processes to valorise organic wastes by converting them to volatile fatty acids. One of the main issues is that certain operational conditions (e.g. pH or different substrate concentrations) can vary significantly the product spectrum. So far, there are no tools that take into the account the characteristic features of cofermentation processes, which hinders the possibility of designing processes that use real wastes as substrates. In this work a mathematical model was developed for the production of volatile fatty acids from organic wastes with a high concentration of carbohydrates and proteins. The model reproduces satisfactorily experimental results and is also able of giving mechanistic insight into the interactions between carbohydrates and proteins that explain the observed changes in the product spectrum. We envision this model as the core of an early-stage design tool for anaerobic cofermentation processes, as shown in this work with different examples.