Systematic methods, such as mathematical programming methods, are traditionally used in decision making concerning capacity planning, especially at tactical and operational level. However, it is the strategic level at which the use of systematic methods might have the greater impact as decisions at this level allocate irreversibly substantial resources. The aim of this work is to propose a mathematical programming methodology that can be used in assisting decision makers to undertake decisions related to the strategic (long term) planning of the valorization of industrial byproduct streams via white biotechnology. The novelty of the work presented is that it incorporates significant details of the bioprocess design at the strategic model and also use is made of a relatively accurate model for estimating the cost of manufacture of the alternative bioprocesses. An extensive case study is presented to demonstrate the advantages of the proposed systematic methodology.