Biobased slurry processes and large-scale continuous chemical production share many similarities. These concern not only process technologies and equipment but also staffing (positions/educations) and plant operations, including methods and technologies for planning, scheduling, and control. Process Systems Engineering (PSE) approaches have been applied successfully in large-scale chemical production to optimize processes of high complexity. By replacing rules-of-thumb and oversimplified calculations with rigorous quantification and automation, PSE increases the profitability of a wide range of processes. Such improvement potential also exists in the bioindustry, which traditionally comprises many small-scale and batch plants deployed in food or pharmaceutical production. The article elucidates the most important operational challenges of such processes. It brings together academic research and industrial perspectives by contrasting a careful revision of literature with a survey of personnel working in industrial biobased production settings in Denmark. This analysis allows showing the existence of a gap between academic research focus and industrial need, for instance, concerning production processes with humans-in-the-loop. Furthermore, differences between chemical and biobased processes are pointed out, highlighting some limitations of applying PSE to biobased processes. A deeper understanding of these limitations is fundamental to assessing risks when identifying process improvement potential. Finally, the article suggests a possible roadmap for the development of frameworks for the optimization of industrial biobased processes based on existing works in chemical processing.