The production of biodiesel, a non-toxic liquid fuel that has been increasingly used as a replacement or addition to diesel of fossil origin, has recently attracted an increasing attention. One of the best known and most important reaction pathways of biodiesel synthesis, the transesterification reaction, is the subject of numerous studies and was analyzed in this paper. As one of the new reactor systems for biodiesel production by transesterification, microreactors have increased interest and application. To demonstrate transerterification reaction in microreactors, as well as in other reaction systems, it is necessary to determine the optimal reaction conditions needed in order to obtain yields and content of fatty acid methyl esters in accordance with relevant standards. As a starting material in the production of biodiesel, various oils and fats of natural origin are commonly used, and as a result of the transesterification process, a product is obtained that contains components that need to be separated in order to obtain the purity of biodiesel in accordance with relevant standards. Purpose of this work was biodiesel production of purity defined by relevant quality standards. An integrated microsystem was developed in which the transesterification reaction was firstly carried out in the microreactor leading to the purification of biodiesel in a microsystem connected in series. Purification was performed in a microextractor using a deep eutectic solvent that removes residual reactants and produced glycerol where in the same time biodiesel of high purity is obtained. Lipase, which was used to carry out the transesterification reaction was immobilized on magnetic nanoparticles, which enabled enzyme retention in a microreactor and consequently facilitated the process of purification of biodiesel integrated microsystem and made the process economically sustainable. Inactivation of the enzyme by methanol, another reactant in the transesterification process which is generally added in excess, is one of the primary challenges of enzyme-catalyzed transesterification processes. As one of the possible process solutions, a microreactor system was used in which pure methanol and emulsion of oil and enzyme were used as process inlets where biodiesel was produced with a yield of 94 % for the retention time of 𝜏 = 20 min. Additionally, an integrated system was developed by combining the microreactor with a microextractor. In this system biodiesel was produced with a yield of 94 % for the retention time of 𝜏 = 20 min, and with glycerol content of 0,019 % (w/w).