Implanted rat bones play a key role in studies involving fracture healing, bone diseases or drugs delivery among other themes. In most of these studies the implants integration also depends on the animal daily activity and musculoskeletal loads, which affect the implants mechanical environment. However, the tissue adaption to the physiological loads is often filtered through control groups or not inspected. This work aims to investigate experimentally and numerically the effects of the daily activity on the integration of implants inserted in the rat tibia, and to establish a physiological loading condition to analyse the peri-implant bone stresses during gait. Two titanium implants, single and double cortex crossing, are inserted in the rat tibia. The animals are caged under standard conditions and divided in three groups undergoing progressive integration periods. The results highlight a time-dependent increase of bone samples with significant cortical bone loss. The phenomenon is analysed through specimen-specific Finite Element models involving purpose-built musculoskeletal loads. Different boundary conditions replicating the post-surgery bone-implant interaction are adopted. The effects of the gait loads on the implants integration are quantified and agree with the results of the experiments. The observed cortical bone loss can be considered as a transient state of integration due to bone disuse atrophy, initially triggered by a loss of bone-implant adhesion and subsequently by a cyclic opening of the interface