Microbiome-based anaerobic fermentations are promising platform technologies to convert low grade biomass into chemical building blocks. However, systematic investigations on their scalability are scarce. Here, microbiome-based production of medium-chain carboxylic acids from acetate and ethanol was systematically investigated across scales from serum bottles (110 mL) to standard bioreactors (2.2 L) in batch mode. Microbiome cultivation on serum bottle level for high throughput screening led to a considerable total medium-chain carboxylic acids concentration of 843.2 ± 20 C mM with 77.0 ± 2 mM n-butyrate and 89.2 ± 2 mM n-caproate. Introducing agitation significantly enhanced the maximum product formation rates of n-butyrate (r_C4,max) and n-caproate (r_C6,max) and was identified as a key parameter for further upscaling. The highest total medium-chain carboxylic acids concentration of 977.8 ± 22.8 C mM with 98.5 ± 2.1 mM n-butyrate and 97.3 ± 2.4 mM n-caproate was reached in the 2.2 L standard bioreactor and was only restricted by end-product inhibition. Further, a carbon recovery of up to 94% was independent of the reactor scale proving the transferability of the microbiome and its functions. Based on cloning and sequencing the most abundant microorganisms were closest related to the model organism for microbial medium-chain carboxylic acid formation, Clostridium kluyveri. The current study demonstrates that time and resource efficient screening of functional microbiomes for relevant cultivation conditions on a small scale can be combined with its subsequent upscaling without performance loss.