Biodiesel, which was earlier used only as an alternative fuel, is now an indispensable component of commercial diesel. Conventional production processes are unable to cope with the increasing demand for biodiesel, and therefore more and more work is being done to intensify the existing processes. The intensification of the biodiesel production process, taking into account the environmental and economic factors, is based on increasing productivity. One way to achieve that is by reducing the volume of production units. The application of the enzymatic reaction path, while reducing the volume of process equipment to the micro-level, has significantly magnified the productivity of the biodiesel production process, which is primarily due to better mass transfer in microsystems. Additional breakthrough is the use of deep eutectic solvents (DES) instead of buffers for enzyme stabilization. In this study, a lipase from Thermomyces lanuginosus (TlL) (both commercial and produced by solid-state fermentation) was used as a catalyst for biodiesel production. Edible and waste sunflower oil, as well as methanol, were used as substrates. The reaction mediums were buffer and DES. The transesterification reaction was carried out in a batch reactor and the emphasis was made on different microreactor configurations. The highest yield of 32% for residence time of only τ = 30 min was obtained in the microreactor system with an emulsion of waste oil and a commercial enzyme suspended in a buffer. This indicates that enzymatic transesterification could be a valuable reaction path for dealing with waste oils. Furthermore, biodiesel synthesis in DES showed somewhat lower yields, but by increasing the water content in the system, the reaction could prove much better results. In the end, the effects of reaction conditions on the volumetric productivity of the process were analyzed.