Wheat bread is a widely consumed food and is suitable for the introduction of functional ingredients. The aim of this work was to study the effects of bread with garlic and resistant starch as a fiber source on physiological, metabolic, and functional parameters using an in vivo Wistar rat model. Rats were fed with three diets: a control diet prepared according to the American Institute of Nutrition (C), and two semisynthetic diets containing wheat bread (B) and wheat bread with garlic, resistant starch and calcium citrate (BGR). Fresh feces were weighed and lactobacilli (L) and Enterobacteriaceae (E) were analyzed at different times: 1, 20, 45 and 60 days. The pH of the caecal content was recorded and at the end of the study changes in the bone mineral density of total skeleton (ts BMD), femur (F-BMD), spine (S-BMD) and tibia (T-BMD) were determined. Lipoprotein profile was assessed, atherogenic indexes were calculated and malonaldehyde content was measured in the serum and liver. In relation to gut microbiota, the BGR group showed an increase in the L/E ratio with respect to the other groups which was correlated with a lower cecal pH. Besides, the BGR group presented lower weight and a more favourable metabolic profile. In relation to bone measurements, the BGR group presented higher values of ts BMC, ts BMD, F-BMD, and T-BMD than the B group. Thus, bread with resistant starch, garlic and calcium citrate showed a prebiotic effect increasing calcium bioavailability and deposition in bones, compared with wheat bread. The observed beneficial health effects allow us to consider the design of healthier breads.