The objective of this study was to investigate the potential of supplementing ethanol and lactic acid as electron donors in reverse beta-oxidation for short chain carboxylic acids chain elongation during anaerobic fermentation of acid whey. Best results were achieved when lactic acid was added at concentration of 300 mM. It resulted in medium chain carboxylic acids (MCCAs) concentration of 5.0 g/L. In the trials with ethanol addition, the overall yield was 20% lower. Subsequently liquid-liquid extraction with ionic liquids (ILs) was investigated as a potential purification method of caproic acid. The most promising, with respect to recovery of caproic acid, was piperazinium IL [C(1)C(1)C(10)Ppz][NTF2], however, the selectivity was only 0.39. Less effective [C(1)C(1)C(6)Ppz][NTF2] recovered 85.9% of caproic acid while reaching a higher selectivity of 0.53. Technoeconomic model revealed that to meet the conservative value of $2.25 per kg of caproic acid, the downstream processing should not exceed $0.65 per kg.