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In light of an increasing demand for energy and sustainable development, bioenergy production is a must. A carboxylate platform-based bioprocess now enables the conversion of organic waste into a valuable bioproduct via open culture fermentation due to a complex microbial activity. Caproic acid is one of the promising products that can be further processed into liquid biofuels. In this study we have shown stable, long-term production of n-caproate from acid whey by shaping the reactor microbiome in a UASB bioreactor. The reactor was operated at pH 5.5 with gradually decreasing hydraulic retention time. The results showed acceleration of n-caproate formation and the highest average n-caproate production rate that lasted for 37 days was 134.3 ± 30.9 mmolC L−1 d−1 (0.11 g L−1 h−1) (with a median of 146.1 mmolC L−1 d−1) and specificity between 58 and 83% (with a median of 79%). Microbiological studies showed the prevalence of fermentative microorganisms from the families Coriobacteriaceae, Ruminococcaceae and Prevotellaceae that are the likely agents for lactose and lactate to n-caproate conversion. A flow cytometry based evaluation of the reactor microbiome demonstrated the inherent heterogeneity of microbial subpopulations in terms of microbial activity at different points of fermentation. [ABSTRACT FROM AUTHOR]