Bone, as a tissue, plays a pivotal role in maintaining whole body homeostasis, contributing to, among other things, structural support, blood cell production, and mineral storage. On the other hand, bone homeostasis depends on hormonal factors released by various tissues of the body, including the gastrointestinal tract. Thus, surgical procedures involving the removal of various parts of the stomach wall, such as, antrectomy and fundectomy or partial gastrectomy, may have profound negative effects on bone metabolism and mineralization. These effects may result from changes in the concentration of neuropeptides, such as nesfatin-1, secreted by cells located in the fundus and vestibule of the stomach. Additionally, bone morphogenetic proteins, osteocalcin, osteoprotegerin, and tissue inhibitor of metalloproteinases 2, are regulatory proteins involved in bone metabolism, playing a key role in maintaining the balance between the activity of osteoclasts and osteoblasts, cells responsible for the remodeling of bone tissue. The aim of this study was to investigate the effects of antrectomy, fundectomy, and partial gastrectomy, on bone homeostasis in a rat model. The experiment was carried out on 24 male Wistar rats randomly and equally divided into control (SHO), gastrectomy (GAST), antrectomy (ANT), and fundectomy (FUN) groups. At the beginning of the study, the rats underwent surgical removal of selected parts of the stomach. At the end of the 6-week study, the rats were sacrificed, and femurs were collected. Microscopic images of immunohistochemical reactions (IR) in trabecular and compact bone, as well as isolated articular cartilages and growth plates of femurs were analyzed. The intensity of the immunoreaction (IR) of osteocalcin (OC), osteoprotegerin (OPG), tissue inhibitor of metalloproteinases 2 (TIMP-2), bone morphogenetic protein 2 (BMP-2), and nesfatin-1 was determined, and IR-positive cells were counted in each area of the femur. The quantitative analysis of the intensity of OC IR in growth plate cartilage and trabecular bone showed the highest values after fundectomy in comparison to the other treatments. Moreover, fundectomy increased the intensity of BMP-2 IR in articular cartilage, growth plate cartilage, and trabecular bone. The intensity of OPG IR in articular cartilage and compact bone showed the highest values after antrectomy. The intensity of TIMP-2 IR in the examined parts of the femur was highest in the rats subjected to antrectomy. The intensity of expression of nesfatin-1 IR was highest in articular and growth plate cartilages for rats subjected to gastrectomy. In conclusion, surgical procedures affecting the gastrointestinal tract, such as antrectomy, fundectomy, and partial gastrectomy, can have significant effects on bone metabolism. Our study on a rat model demonstrated varying impacts on bone homeostasis, with different surgeries leading to alterations in the expression of key regulatory proteins involved in bone remodeling.