The rapidly growing world population, the consequences of climate change and conventional agriculture as well as the limited resources of our planet threaten the food supply of humanity, especially with vital proteins. Therefore, innovation of agricultural systems is crucial for global food security and sustainable development. One proposed system is the cultivation of algae in artificially illuminated photobioreactors, which is a promising technology to limit land and water use. To achieve a competitive position between other agricultural systems and to reduce costs in a systematic and proactive approach, we suggest using Target Costing (TC) at an early stage of development. The paper aims to provide an overview of the state of the art in TC of agricultural systems. The authors identify a suitable approach for the economic evaluation of algae cultivation in bioreactors and adapt it specifically for the extraction of proteins. Based on this, different scenarios are discussed how a cost reduction of the existing systems can be achieved. The focus is on the reduction of energy costs, a suitable site selection and the use of side streams and products.