Biotechnology applications have contributed significantly to “factory in a lab” research. Although the largely adopted Design–Build–Test–Learn cycle has considerably improved synthetic biology and metabolic engineering capabilities, we are still far from achieving industrial efficiency. As we are now faced with the challenge of exponential population growth and drastic climatic changes affecting the traditional agriculture, there is an imminent need to optimize biotechnology applications, especially for the alternative food source initiative, which has received immense attention recently. Here, I highlight the importance of multi-disciplinary research, and the need to develop integrated systems biology methods, using high-throughput omics data, dynamic modelling and machine learning techniques, to further enhance the lab-based production process. Moving forward in this direction will likely reduce the overall cost and increase the output for the longer term future.