The effects of elevation, rootstock, and soil depth on the nutritional quality of mandarin oranges from 11 groves in California were investigated by nuclear magnetic resonance (NMR) spectroscopy by quantifying 29 compounds and applying multivariate statistical data analysis. A comparison of the juice from oranges in groves with deeper soil and trifoliate rootstock versus those with shallow soil and C-35 rootstock revealed differences in the concentrations of 4-aminobutyrate, ethanol, phenylalanine, succinate, and isoleucine. A comparison of fruit from trees grown at higher versus lower elevation revealed that those at higher elevation had higher concentrations of amino acids, succinate, and 4-aminobutyrate and lower concentrations of sugars and limonin glucoside. Such differences indicate that rootstock, soil depth, and differences in elevation influence the fruit nutrient composition. This study highlights how metabolomics coupled with multivariate statistical analysis can illuminate the metabolic characteristics of citrus, thereby aiding in the determination of the grove identity and fruit quality during orange production.