Cow manure (CM) generation in large volumes has for long been considered a waste management challenge. However, the organic content of CM signals opportunities for the production of value-added bioproducts such as volatile fatty acids (VFAs) through anaerobic digestion (AD). However, a robust VFAs fermentation process requires effective methane formation inhibition and enhance VFAs recovery. In this study, thermal pretreatment was applied to inhibit methanogens for enhanced VFAs production and an immersed membrane bioreactor (iMBR) for in situ recovery of VFAs in a semi-continuous AD. Maximal VFAs yield of 0.41 g VFAs/g volatile solids (VS) was obtained from thermally-treated CM without inoculum addition. The CM was further fed to the iMBR operating at organic loading rates of 0.8–4.7 gVS/L.d. The VFAs concentration increased to 6.93 g/L by rising substrate loading to 4.7 g VS/L.d. The applied iMBR set-up was successfully used for stable long-term (114 days) VFAs production and recovery.