Aims: The aim of the study was to investigate the isomerization of linoleic (LA) and linolenic acids (LNAs) into their conjugated isomers by Propionibacterium freudenreichii DSM 20270 and utilize this feature for microbial enrichment of blackcurrant press residue (BCPR) with health-beneficial conjugated fatty acids. Methods and Results: First, the ability of P. freudenreichii to isomerize 0·4 mg ml−1 of LA and LNA was studied in lactate growth medium. Free LA and α-LNA were efficiently converted into conjugated linoleic (CLA) and α-linolenic acid (α-CLNA), being the predominant isomers c9,t11-CLA and c9,t11,c15-CLNA, respectively. The bioconversion of α-LNA by P. freudenreichii was more efficient in terms of formation rate, yield and isomer-specificity. Thereafter, free LA and LNAs obtained from hydrolysed BCPR neutral lipids, by lipolytically active oat flour, were subjected to microbial isomerization in BCPR slurries. In 10% (w/v) slurries, a simultaneous enrichment in c9,t11-CLA and c9,t11,c15-CLNA of up to 0·51 and 0·29 mg ml−1 was observed from starting levels of 0·96 mg LA ml−1 and 0·37 mg α-LNA ml−1 respectively. Conclusions: This study shows that growing cultures of P. freudenreichii DSM 20270 are able to simultaneously enrich BCPR with health-beneficial conjugated isomers of LA and α-LNA. Significance and Impact of the Study: This study demonstrates that microbial isomerization technique can be utilized to enrich lipid-containing plant materials with bioactive compounds and thereby enable valorization of low value plant-based side streams from food industry into value-added food ingredients.