The recombinant Bacillus megaterium strain WH323 was employed for the inducible production and secretion of recombinant Thermobifida fusca hydrolase (TFH). Continuous cultivations were carried out in a chemostat using either glucose or pyruvate as sole carbon source. A remarkable increase of produced TFH was detected for the pyruvate-dependent cultivation compared to glucose-dependent growth. Estimation of intracellular carbon fluxes through the central metabolism for both growth conditions using (13)C-labelled substrates revealed noticeable changes of the fluxes through the tricarboxylic acid cycle, the pentose phosphate pathway and around the pyruvate node when protein production was induced. With pyruvate as sole carbon source the observed alterations of the fluxes yielded an increased production of ATP and NADPH both required for the anabolism. Additionally, the analysis of the corresponding secretome revealed significantly reduced amounts of extracellular proteases in the medium compared to glucose-grown cultivations. Thus, pyruvate-dependent chemostat cultivation was identified as a favourable condition for production and secretion of recombinant TFH using B. megaterium as production host.