Metabolomics is useful for evaluating the fundamental mechanisms of improvements in the health functions of the elderly. Additionally, gardening intervention as a regular physical activity for the elderly maintained and improved physical, psychology, cognitive, and social health. This study was conducted to determine whether the cognitive ability of the elderly is affected by participating in a gardening activity program as a physical activity with a metabolomic potential biomarker. The gardening program was designed as a low to moderate intensity physical activity for the elderly. Serum metabolites resulting from gardening were subjected to metabolite profiling using gas chromatography time-of-flight mass spectrometry and ultra-high-performance liquid chromatography-linear trap quadruple-orbitrap-mass spectrometry followed by multivariate analyses. The partial least squares-discriminant analysis showed distinct clustering patterns among the control, non-gardening, and gardening groups. According to the pathway analysis, tryptophan metabolism including tryptophan, kynurenine, and serotonin showed significantly distinctive metabolites in the gardening group. Brain-derived neurotrophic factor levels (BDNF) in the gardening group were significantly increased after the gardening program. Correlation map analysis showed that the relative levels of tryptophan metabolites were positively correlated with BDNF. Our results show that tryptophan, kynurenine, and serotonin may be useful as metabolic biomarkers for improved cognitive ability by the gardening intervention.