Lipase from Rhizopus oryzae immobilized on polysiloxane-poly(vinyl alcohol) (SiO2-PVA) was used to study the interesterification reaction of the milkfat with soybean oil in a stirred tank reactor (STR) containing baskets for the immobilized enzyme retention in two different configurations: central or lateral. The progress of the reaction was followed by determining free fatty acids, composition in triacylglycerols (TAGs), and consistency. The central basket was chosen for assessing the biocatalyst operational stability by running 10 consecutive batch assays lasting 6 h each. Non-notable deactivation of the biocatalyst was observed during the total operation time (60 h). The potential of the evaluated system to make the milkfat-based fat more spreadable under cooling temperature and with lower saturated fatty acids content was demonstrated in this study. Both evaluated basket reactor designs have shown potential to be used in interesterification reactions of industrial interest.