Bicarbonate has long been touted as a putative ergogenic aid that improves exercise performance and blood buffering capacity during strenuous exercise. However, the underlying mechanisms of action of bicarbonate intake on skeletal muscle metabolism have yet to be fully elucidated. Herein, we apply two orthogonal analytical platforms for nontargeted profiling of metabolites and targeted analysis of electrolytes from mass-limited muscle tissue biopsies (∼2 mg dried mass) when multisegment injection-capillary electrophoresis-mass spectrometry (MSI-CE-MS) and CE with indirect UV detection are used, respectively. Seven untrained men performed a standardized bout of high-intensity interval exercise trial following either bicarbonate (0.40 g/kg) or placebo ingestion in a double-blinded, placebo-controlled, crossover study design, where paired skeletal muscle tissue and plasma specimens were collected at three time intervals at rest, postexercise, and recovery. Optimization of a quantitative microextraction procedure was first developed for lyophilized tissue prior to characterization of the human muscle metabolome, which resulted in the identification and quantification of more than 80 polar/ionic metabolites reliably (CV < 30%) detected in a majority (>75%) of samples with quality control. Complementary univariate and multivariate statistical methods were used to identify biomarkers associated with strenuous exercise and/or bicarbonate treatment responses, whereas structural elucidation of biologically significant intramuscular metabolites was performed using high-resolution MS/MS. Importantly, bicarbonate ingestion prior to strenuous interval exercise was found to elicit a modest treatment effect ( p < 0.05) in comparison to placebo on metabolic pathways associated with ionic homeostasis (potassium), purine degradation (uric acid), and oxidative stress as regulated by glutathione metabolism (oxidized mixed glutathione disulfide) and histidine-containing dipeptides (anserine) within muscle tissue that was distinctive from dynamic metabolic changes measured in circulation. This work provides deeper biochemical insights into the effect of acute alkalosis in preserving contracting muscle function during high-intensity exercise, which is also applicable to the study of muscle-related pathologies relevant to human health and aging.