Chain elongation fermentation can be used to convert organic residues into biobased chemicals. This research aimed to develop a bioprocess for branched medium chain fatty acids (MCFAs) production. A long-term continuous reactor experiment showed that iso-caproate (4-methyl pentanoate, i-C6) can be produced via ethanol based chain elongation. The enriched microbiome formed iso-caproate from iso-butyrate at a rate of 44 ± 6 mmol C L-1 day-1 during the last phase. This amounted to 20% of all formed compounds based on carbon atoms. The main fermentation product was n-caproate (55% of all carbon), as a result of acetate and subsequent n-butyrate elongation. The microbiome preferred straight-chain elongation over branched-chain elongation. Lowering the acetate concentration in the influent led to an increase of excessive ethanol oxidation (EEO) into electron equivalents (e.g., H2) and acetate. The formed acetate in turn stimulated straight chain elongation, but the resulting lower net acetate supply rate towards straight chain elongation led to an increased selectivity towards and productivity of i-C6. The electrons produced via oxidation routes and chain elongation were apparently utilized by hydrogenotrophic methanogens, homoacetogens, and carboxylate-to-alcohol reducing bacteria. Further improvements could be achieved if the acetate-producing EEO was minimized and limitations of ethanol and CO2 were prevented.