Background Autophagy, which is stimulated by cellular or environmental stresses, is involved in several distinct biological processes, and the regulation mechanism is complex. Autophagy has been reported to modulate immune system components. In the present study, the expression of Beclin-1 and LC3, an autophagy-related proteins, and its relationship with FOXP3 expression were investigated in gastric adenocarcinoma cells and FOXP3+T cells (regulatory T cells). Methods Tissue samples were acquired from 182 cases of gastric adenocarcinoma that were surgically resected at Kyung Hee University Hospital at Gangdong from 2006 to 2012. Immunohistochemical staining for Beclin-1, LC3, FOXP3, and CD8 was performed. Results Consequently, positive Beclin-1 expression was significantly associated with a smaller tumor size, mixed histologic type, better histologic grade, lower T category, lower N category, lower recurrence rate, less lymphatic invasion, less vascular invasion, and less neural invasion. Positive tumoral FOXP3 expression was significantly associated with a lower T category, lower N category, lower recurrence rate, and less lymphatic invasion. The cases of more infiltrated Tregs (≥ 25/high power field, HPF) significantly correlated with a lower N category, lower recurrence rate, less lymphatic invasion, more infiltrated CD8+T cells, and a higher number of tumor-infiltrating lymphocytes. Beclin-1 and LC3 expression were positively correlated with tumoral FOXP3 overexpression. In addition, Beclin-1 expression was significantly associated with a greater number of infiltrated Tregs in gastric adenocarcinoma. Both the positive Beclin-1 expression and positive tumoral FOXP3 expression cases showed significantly better disease-free and overall survival. In addition, the patients with an increased number of infiltrated Tregs (≥ 25/HPF) showed better disease-free and overall survival rates. Conclusion In conclusion, the autophagic function of Beclin-1 in gastric adenocarcinoma cells was associated with an increased number of infiltrated Tregs and tumoral FOXP3 containing tumor suppressor function. Therefore, the favorable effects of Beclin-1 expression in gastric adenocarcinoma is associated with the regulation of Tregs and tumoral FOXP3 expression.