In citrus, fruit bearing affects floral induction and the nutritional condition of the tree. For this reason, bearing too many or too few fruit causes fluctuation in flower number the following spring. This in turn leads to annual alternation between rich and poor crops, known as alternate bearing. To identify the metabolites related to alternate bearing, quantitative metabolomics analysis was conducted with stem tissues of vegetative shoots collected in November. Twelve Satsuma mandarin trees bearing different amounts of fruit were used in this study. Fruit weight per leaf area of these trees was significantly and negatively correlated with the expression of a flowering-related gene, citrus FLOWERING LOCUS T, in the stem in November and the number of flower buds the following spring. In metabolomics analysis, adenosine triphosphate was detected at high concentrations in lightly fruiting trees. Other coenzymes such as uridine triphosphate, nicotinamide adenine dinucleotide phosphate, and ascorbic acid were also more abundant in the off-crop trees. In addition, the off-crop trees accumulated sugar phosphates such as fructose 6-phosphate, glucose 6-phosphate, and ribulose 1,5-diphosphate. Furthermore, heavily fruiting trees accumulated more amino acids. These results indicate that fruit bearing affects the metabolism of coenzymes, sugars, and amino acids in the stem of vegetative shoots.