CLA refers to a group of geometrical and positional isomers of linoleic acid (LA) with conjugated double bonds. CLA has been reported to have diverse health benefits and biological properties. Traditional organic synthesis is highly capital-intensive and results in an isomeric mixture of CLA isomers. Biotechnology presents new alternatives to traditional lipid manufacturing methods. The objective of this study was to examine the effect of protein isolation procedures on linoleate isomerase (LAI) recovery from microbial cells and biocatalysis of LA to CLA. Protein isolation experiments were carried out using Lactobacillus acidophilus L1 and two strains of Lactobacillus reuteri (ATCC 23272 and ATCC 55739). Under the same assay conditions, ATCC 55739 had the highest LAI activity among the microbial cultures examined in this study. Efficiency of cell lysis methods, which included various combinations of lysozyme and mutanolysin treatments in combination with sonication and osmotic rupture of cells with liquid nitrogen, was very low. Although treatment of cell material with a detergent (octylthioglucoyranoside) freed a significant amount of LAI activity into the solution, it was not sufficient to recover all the LAI activity from the residual cells. Crude LAI preparations produced mainly the cis-9,trans-11 CLA isomer. Time and substrate/protein ratio had a significant effect on biocatalysis of LA to CLA. It appears that the mechanism and kinetics of enzymatic conversion of LA to CLA are quite complex and requires further research using pure LAI preparations.