Sleeve gastrectomy typically leads to weight loss, including a reduction in fat-free mass (FFM). Studies have shown significant FFM loss within 1 year after the procedure but with individual variations. This study aimed to assess whether preoperative amino acid metabolite levels can predict FFM changes following sleeve gastrectomy. This study involved 42 patients. Body weight, fat mass (FM), and FFM were measured preoperatively and 3, 6, and 12 months postoperatively. All participants experienced weight loss, FM reduction, and FFM decrease for up to 3 months after surgery. However, the following distinct groups emerged from 3 to 6 months postoperatively: one showed FFM gain relative to weight loss, whereas the other exhibited continued FFM reduction relative to weight loss. This trend persisted for up to 12 months postoperatively and became more pronounced. The group with FFM gain had lower preoperative BMI and higher levels of indole-3-pyruvic acid (IPyA). Logistic regression and ROC curve analyses confirmed IPyA's ability to predict FFM gain between 3 and 6 months after sleeve gastrectomy, with a useful cutoff value of 20.205. Preoperative IPyA levels were associated with FFM gain relative to weight loss in the 3 to 6 months following sleeve gastrectomy. These findings suggest that IPyA may be a potential predictor for FFM changes during this period.