We have developed an online, high-throughput, microdialysis-capillary electrophoresis (MD-CE) assay for measuring the in vivo dynamics of amino acid biomarkers of metabolism in adipose tissue. Microdialysis probes were implanted into the inguinal adipose tissue depot of C57BL6 mice. The probe location and integrity were verified following each experiment, demonstrating our ability to accurately target the inguinal adipose tissue depot without damaging the probe. The relative concentrations of small molecule bioamines were measured in adipose tissue every 22 s. Arginine, lysine, isoleucine, leucine, methionine, phenylalanine, valine, GABA, glutamine, alanine, glycine and taurine were separated and detected at concentrations significantly higher than the assay LOD. The relative abundances of these analytes were found to be reproducible between mice. The capability of the online MD-CE assay to record dynamic, in vivo changes was assessed by administering an insulin stimulation via tail vein injection. Valine concentrations increased by 40% in response to insulin exposure, while alanine increased by 46% and taurine increased by 37%. Following the initial increase, the amino acid concentrations remained significantly elevated for an extended period (p < 0.001).