Siraitia grosvenorii (monk fruit) is a cucurbitaceous plant endemic to China that serves as both food and medicine. Its fruit accumulates mogrosides, zero-calorie natural sweeteners approximately 300-fold sweeter than sucrose that are widely used in food and beverages. Whereas tissue-culture studies of S. grosvenorii have focused largely on regenerated plantlets, the metabolic events underlying tuber formation in vitro remain poorly characterized. Here, we combined morphological observation, quantification of starch and soluble sugars, time-series transcriptomics, and widely targeted metabolomics to dissect metabolic reprogramming during in vitro tuberization of S. grosvenorii. Visible tuber structures emerged at 45 days post-inoculation and accumulated starch continuously throughout development. Starch and sucrose metabolism and flavonoid biosynthesis acted as core pathways regulating the accumulation of carbohydrates and flavonoids. Candidate MYB, bHLH, and ERF transcription factors were screened to explore putative upstream regulation of these metabolic changes. Our results demonstrate that in vitro tuber formation of S. grosvenorii is a multi-stage, highly coordinated process, and provide a molecular basis for breeding high-quality propagation materials and for exploiting this species as a source of functional food ingredients and natural sweeteners.