BACKGROUND: The high rate production of n-caproic acid (C6) through chain elongation can be achieved with the use of pertraction systems for the continuous and selective extraction of C6. However, although the biological conversion processes are enhanced at a neutral pH, high extraction efficiency depends on acidic conditions. Understanding of these divergent pH effects is fundamental for a reliable operation and scale-up of these C6-producing systems. RESULTS: A bench-scale anaerobic filter (12.8 L) fed with fermented sugarcane at organic loading rates of ≈7.2 g of chemical oxygen demand (COD) L −1 day −1 achieved C6 production rates of 2.1 and 3.8 g COD L −1 day −1 , without and with in-line extraction, respectively. Compared to previous studies, a high average extraction rate of 24.7 g COD m −2 day −1 was observed due to a high reactor volume-to-membrane-area ratio. The novel model described here with biological and pertraction processes for continuously operated systems indicates that an optimal operative pH can simultaneously maximize C6 production and extraction. The hydraulic retention time was another key parameter for balancing inhibition by undissociated C6 and losses due to nonextracted C6. CONCLUSIONS: Sugarcane biorefineries can produce C6, which has a market value that is >10-fold higher than ethanol. Simulations of chain elongation processes require the implementation of hydrogenotrophic methanogens to allow for a comprehensive description of ethanol consumption together with the C6 formation, in-line C6 extraction processes, and formation of gaseous by-products. Although these simulations were possible using parameter sets from the literature, further studies are needed for parameter identification, especially under inhibition at low pH.