Traditionally, the main objective of microbial strain engineering has been to enhance key performance indicators, such as titers, rates, and yields of whole-cell biocatalysts by metabolic engineering. Often, the focus has been primarily on the whole-cell biocatalyst, neglecting the conditions of the process in which the microorganism must eventually perform, potentially leading to exacerbated scaling and resulting inefficiency. A comprehensive perspective on the entire process chain connecting strain engineering with up- and downstream processing, already in the early stages of process development, with the goal of a functioning bioprocess in mind, can be beneficial. In this chapter, we describe exemplary use cases in which strain engineering was not solely focused on improving the whole-cell biocatalyst’s ability for production but was guided by the processing strategy. Highlights include the alteration of cell morphology to enhance performance in bioreactors and facilitate downstream processing, or the engineering of strain robustness to improve substrate uptake. Finally, we give a perspective on how a comprehensive view of bioprocessing will foster the emerging sustainable bioeconomy.