A　method　using　high-speed　capillary　micellar　electrokinetic　chromatography　and　a　microbial　fuel　cell　was　applied　to　determine　the　metabolite　of　the　peptides　released　by　Bacillus　licheniformis.　Two　peptides,　l-carnosine　and　l-alanyl-l-glutamine　were　used　as　the　substrate　to　feed　Bacillus　licheniformis　in　a　microbial　fuel　cell.　The　metabolism　process　of　the　bacterium　was　monitored　by　analyzing　the　voltage　outputs　of　the　microbial　fuel　cell.　A　home-made　spontaneous　injection　device　was　applied　to　perform　high-speed　capillary　micellar　electrokinetic　chromatography.　Under　the　optimized　conditions,　tryptophan,　glycine,　valine,　tyrosine　and　the　two　peptides　could　be　rapidly　separated　within　2.5 min　with　micellar　electrokinetic　chromatography　mode.　Then　the　method　was　applied　to　analyze　the　solutions　sampled　from　the　microbial　fuel　cell.　After　92　h　running,　valine,　as　the　metabolite,　was　successfully　detected　with　concentration　3.90 × 10−5　M.　The　results　demonstrated　that　Bacillus　licheniformis　could　convert　l-carnosine　and　l-alanyl-l-glutamine　into　valine.　The　method　employed　in　this　work　was　proved　to　have　great　potential　in　analysis　of　metabolites,　such　as　amino　acids,　for　microorganisms.　©　2017　WILEY-VCH　Verlag　GmbH　&　Co.　KGaA,　Weinheim