With advances in surgical treatment for gastric cancer and improvements in long-term prognosis, increasing attention has been directed toward late nutritional complications. This retrospective study focused on body composition as an indicator of nutritional status, aiming to elucidate mid- to long-term changes following minimally invasive gastrectomy (MIG). A total of 102 3-year cancer survivors who underwent curative laparoscopic or robotic gastrectomy were included. Body composition indices, including subcutaneous fat, visceral fat, and skeletal muscle, were calculated using multidetector computed tomography images. All indices decreased relative to preoperative levels and remained lower during long-term postoperative follow-up. The reduction was more pronounced during the mid-term period. Although the body fat indices demonstrated a slight trend toward recovery, skeletal muscle showed persistently reduced levels in the long term. Multiple regression analysis revealed that only total gastrectomy (MITG) was identified as an independent predictor of reductions in all indices (all P < 0.01). When stratified by the extent of gastrectomy, the postoperative values of all indices were lower in the MITG group than in the distal gastrectomy group. To address late nutritional complications following MIG, particular attention should be paid to the mid-postoperative period, when nutritional status reaches its lowest point, as well as to patients undergoing MITG.