A cost analysis of enzymatic biodiesel production in small-scaled packed-bed reactors using refined sunflower oil is performed in this work. A few enzymatic micro-flow reactors have so far reached a performance close to gram-scale, which might be sufficient for the pharmaceutical industry. This study, motivated by the availability of new immobilization materials and techniques, wants to go one step further and explore the application of enzymatic micro-flow reactors to the biofuel market, which is much larger in volume. However, there are certain hurdles which need to be overcome to ensure commercialization of this process; this requires a simultaneous multi-innovation approach, which has been reviewed in the introduction. A detailed analysis of the two main hurdles – lipase production & immobilization, and severe mass transfer limitations – along with the state-of-the-art, and forecasted innovations, has also been provided. The basic input data for the cost evaluation was taken from performance data of enzymatic micro-flow reactors published in literature, and certain assumptions (based on this data). The costs of enzymatic biodiesel production are also benchmarked against those of a real biodiesel production plant. It is found that a major cost for the scaled-up flow case is the enzyme cost. This is intrinsic to the approach adopted here; it adds process intensification value (here towards new resources: waste oils), and has to be accepted. Yet, an even bigger cost issue is the support material itself. The current costs of the commercial available Eupergit CM polymeric resin may allow its use in pharmaceutical manufacturing, but are prohibitively high for large-volume biodiesel production. The use of a similarly-functional polymer, which is simple to manufacture and lower in costs, is strongly advised, and we have chosen the SEPABEADS EC-EP/M carrier for this. An optimistic scenario is proposed with the following assumptions: use of the cheap SEPABEADS EC-EP/M carrier, utilization of refined sunflower oil as raw material, improved immobilization efficiency in regard to higher activity retention and enzyme loading, and increase in number of reuse of immobilized lipase. Following this, a production scenario for the enzyme-based biodiesel processing using refined sunflower oil at 10,000 t/a capacity can be made using 32 parallel reactors with 10 cm diameter and 100 cm length.