TgF344-AD is a transgenic rat model of Alzheimer’s disease (AD) that shows all its pathological hallmarks in a progressive way. A cohort of transgenic rats and their control littermates were scanned at different time-points from early adulthood to aged animals, including spectroscopy and diffusion-weighted MRI. Acquisitions were processed to obtain regional structural connectivity parameters and metabolite concentrations in hippocampus and striatum. Decrease in network metrics in both regions at different ages, and increases in glutamine and decreases in glutamate, NAA, NAAt and taurine were observed in the transgenic group. Thus, multimodal MRI can improve characterization of different AD stages.